The molecular participants of the defense response to the necrotrophic fungus Alternaria alternata on cultivated and wild tomato

Tomato (Solanum lycopersicum L.) is one of the world’s most valuable vegetable crops, but its production is increasingly threatened by fungal pathogens—particularly Alternaria spp., which cause early blight and brown spot disease complex (EBDC). These necrotrophic fungi kill host tissue and thrive under changing climate conditions, leading to major yield losses and widespread fungicide use. Current cultivars lack strong genetic resistance, making the development of durable, sustainable defense strategies an urgent agricultural priority. We used gene regulatory networks (GRNs) and weighted gene co-expression network analysis (WGCNA) to analyze the transcriptional landscape of resistance to EBDC. This dissertation addresses this challenge by investigating resistance to EBDC through a multi-scale lens, combining quantitative phenotyping, network biology, and wild tomato diversity. It focuses on Solanum chilense, a wild relative of the cultivated tomato. Notably, resistant genotypes exhibited strong transcriptional activity and early activation of defense modules, while susceptible genotypes showed weak, fragmented networks. Temporal network rewiring and module preservation analyses further emphasized that effective resistance relies not just on the presence of defense genes but on their dynamic regulatory coordination. We used high-throughput quantitative phenotyping to capture subtle differences in infection progression across 124 S. chilense accessions. By leveraging phenotypic diversity to resolve resistant/susceptible gene network topologies, this dissertation advances both the understanding of necrotrophic pathogen resistance and the tools available to improve it. The findings highlight S. chilense as a rich source of resistance alleles and demonstrate the potential of systems biology to breed crops with resilience to complex pathogens in the future.

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