Towards Deciphering the Wheat-Tan Spot Pathosystem Through a Systems Biology Approach

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Student thesis: Doctoral ThesisDoctor of Philosophy

Original languageEnglish
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Award date2022
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Tan Spot is a yield-reducing foliar disease caused by the fungus Pyrenophora tritici-repentis (Ptr), occurring in various cereals but most importantly in wheat. Despite being a real threat to global wheat production, this pathosystem has yet to be examined systemically and by systems biology approaches. Eight parents of a wheat MAGIC (multiparent advanced generation intercross) population and two Brazilian commercial cultivars (namely Fundacep Horizonte and PF 080719) were screened against ToxA-producing Ptr strains. The lines exhibited differential levels of resistance, with the parental line Hereward being the most susceptible, and Robigus the most resistant. Analyses of infected leaves of the eight parental lines by RGB-imaging and of Robigus and Hereward by fluorescence microscopy suggested that cell wall appositions were a distinctive feature in the genotype with increased Ptr resistance. Assessing RNA-seq data acquired from Robigus and Hereward at 0, 48, and 96 h post-inoculation with Ptr (or mock-inoculated), identified differentially expressed genes (DEG) which could be associated with significantly enriched pathways associated with cytoskeleton reorganization and actin
polymerisation (amongst others) exclusively in Robigus. In vivo treatment with an actin polymerisation inhibitor resulted in increased number of lesions in all genotypes but lesions did not grow in size, suggestive of additional defence mechanisms. Correlation-based integration of transcriptomics and metabolomics provided further evidence of cell wall modifications and chitinase activity in Robigus, whereas downregulated energy-related pathways were found enriched in Hereward. Exogenous applications of salicylic acid and auxin resulted in increased susceptibility of Robigus to Ptr. This, alongside observations from transcriptomics analysis, suggested that both hormones increased susceptibility to Ptr.
Interestingly, an unsupervised co-expression network analysis revealed a common set of reactions triggered by Ptr in Robigus and Hereward, which included the activation of pathogenesis-related proteins and enzymes involved in the biosynthesis of flavonoids. This pathway is a key distinguishing genotypic feature between the two Brazilian spring-wheat cultivars differing in their ability to suppress Ptr infections. The spring wheat cultivar PF 080719 exhibited increased resistance to Ptr infection at the seedling stage, but it was susceptible at the reproductive stage. The spring wheat cultivar Fundacep Horizonte was consistently susceptible to Ptr at either growth stage. Metabolomic analyses of flag leaves
showed that only 7.9% of total responses were shared between both Brazilian plants, and each cultivar had a unique set of metabolic responses to Ptr infection. These changes were summarised with the enrichment of biosynthesis of flavonoids and bioenergetic metabolism, among others. Altogether, this “top-down” systems biology approach to study wheat immunity towards Ptr has yielded high-confidence candidate genes and metabolic processes underpinning defences against the Tan Spot disease leading to partial resistance and susceptibility.