Abstract
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
Highlights
Wild Solanum species are alternative hosts for pathogens of cultivated potato, which is a crop attacked by many different microorganisms
Based on a detached leaf resistance assay with P. infestans performed as described in Ali et al (2012) one individual from each wild Solanum species and the three potato clones were selected for transcriptome profiling
We found no less than 134 RXLR effectors of the pathogen in the susceptible S. physalifolium (Table 5; Table S8), whereas no P. infestans effectors were detected in S. dulcamara and Sarpo Mira, indicating an efficient early defense response by both hosts upon perceiving the pathogen associated molecular patterns (PAMPs)
Summary
Wild Solanum species are alternative hosts for pathogens of cultivated potato, which is a crop attacked by many different microorganisms. Local populations of these often grow in close proximity of potato fields. Compared to cultivated potatoes, which are not well adapted to the local environment and might have lost important genetic variation through domestication, wild species could be a source for desirable traits to breed disease-resistant varieties of the crop. In the last few decades, many resistance (R-)genes against this devastating pathogen have been successfully transferred from various wild Solanum species to potato (Vleeshouwers et al, 2011; Rodewald and Trognitz, 2013). The pathogen contains fast-evolving effector genes localized in a highly dynamic region of its genome (Haas et al, 2009), enabling it to quickly overcome the R-gene based resistance in potato
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