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

Abstract

ABSTRACTMildew locus a (Mla) from the Triticeae grain crop barley (Hordeum vulgareL.) 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 withBhto infer gene effects and epistatic relationships governed by theMla6NLR, two other host loci critical to the interaction,Blufensin1(Bln1) andRequired for Mla6 resistance3 (Rar3),and genes that interact with them.Bln1is anR-gene independent regulator of immunity and the resistantbln1mutant exhibits enhanced basal defense to compatibleBh.Rar3is required for MLA6-mediated generation of H2O2and the hypersensitive reaction; therar3mutant contains an in-frame Lys-Leu deletion in the SGT1-specific domain that compromises immunity by a subset ofMlaalleles. Interactions ofMla6andBln1resulted in symmetric, suppression and masked epistasis on theBh-induced barley transcriptome. Likewise, dominant or equal effects were caused byMla6andSgt1.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 correspondingBhinfection transcriptome was classified into nine co-expressed modules, linking differential expression with pathogen development. Expression of most of 517Bheffectors 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.