Transcriptome-based host epistasis and pathogen co-expression in barley-powdery mildew interactions

Mildew locus a (Mla) from the Triticeae grain crop barley (Hordeum vulgare L.) encodes a multi-allelic series of nucleotide-binding leucine-rich repeat (NLR) immune receptors. These variable NLRs recognize complementary secreted effectors from the powdery mildew fungus, Blumeria hordei (Bh), to block disease progression. We used a dynamic time-course transcriptome of barley infected with Bh to infer gene effects and epistatic relationships governed by the Mla6 NLR, two other host loci critical to the interaction, Blufensin1 (Bln1) and Required for Mla6 resistance3 (Rar3), and genes that interact with them. Bln1 is an R-gene independent regulator of immunity and the resistant bln1 mutant exhibits enhanced basal defense to compatible Bh. Rar3 is required for MLA6-mediated generation of H2O2 and the hypersensitive reaction; the rar3 mutant contains an in-frame Lys-Leu deletion in the SGT1-specific domain that compromises immunity by a subset of Mla alleles. Interactions of Mla6 and Bln1 resulted in symmetric, suppression and masked epistasis on the Bh-induced barley transcriptome. Likewise, dominant or equal effects were caused by Mla6 and Sgt1. Of a total of 468 barley NLRs, 366 were expressed in our dataset and 115 of those were grouped under different gene effect models, which localized to several chromosome hotspots. The corresponding Bh infection transcriptome was classified into nine co-expressed modules, linking differential expression with pathogen development. Expression of most of 517 Bh effectors exhibited dependence on disease phenotype and was associated with appressorial or haustorial structures, suggesting that disease is regulated by a host-pathogen intercommunication network that diversifies the response.