Affiliations: 1) Iowa State University, Ames, IA; 2) Informatics Infrastructure Team, Tree of Life Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; 3) Phytoform Labs, Rothamsted Research, Harpenden, UK; 4) Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA
Keywords: Genetic interactions
Plant disease resistance often occurs upon direct or indirect recognition of pathogen effectors by host nucleotide-binding leucine-rich-repeat (NLR) receptors. The Triticeae grain crop barley has evolved a diverse series of NLR receptors, including those encoded by Mildew resistance locus a (Mla), which are complementary to effectors secreted by the powdery mildew fungus, Blumeria graminis f.sp. hordei (Bgh). Mla is essential to a complex gene interaction network that leads to life or death of the host. Epistasis models help to explain those relationships by calculating gene effects on the phenotype and classifying them as additive or the product of gene interaction(s). Here, we used a dynamic transcriptome collected from the interaction between barley and Bgh to propose models to infer gene effects and epistatic relationships among Mla6 and two additional host genes critical to the interaction, Blufensin1 (Bln1) and Rar3 (Sgt1). Bln1 is a negative regulator of immune signaling and the resistant bln1 mutant exhibits enhanced basal defense. Rar3 (required for Mla6 resistance3) is required for MLA6-mediated generation of H2O2 and the hypersensitive response. The susceptible rar3 mutant contains an in-frame Lys-Leu deletion in the SGT1-specific domain, which interacts with NLR proteins. The first model contains data from single and double immune mutants allowing for the calculation of epistatic effects between Mla6 and Bln1 and demonstrating their genetic interaction. The second model between Mla6 and Sgt1, proposed from single mutant data, revealed that both genes have dominant and equivalent effects to control barley gene expression. In contrast, most of the Bgh transcriptome showed dependence on the disease phenotype while some genes would fit the Mla6:Bln1 epistatic- or Mla6:Sgt1 dominant responses, suggesting that its expression is regulated by host-pathogen intercommunication. Genomic location was proposed as a regulation mechanism of the gene effects by associating chromosome hotspots with different genetic effect patterns. Lastly, two gene families were characterized under the models, NLRs for barley and effectors for Bgh, which determine the outcome of the host-pathogen interaction. Results from this analysis point to a large perturbation network of the host and pathogen arsenals under different genetic mechanisms that diversify expression patterns and increase robustness of the response.