Gene expression profiling of virulence-associated proteins in planta during net blotch disease of barley

The proteinaceous extracts of culture filtrates from Pyrenophora teres f. teres (Ptt) have been previously shown to induce symptoms on susceptible barley cultivars suggesting these fungal proteins are likely to contribute to net form net blotch (NFNB) disease. This research primarily aimed to study the in planta gene expression of 222 proteins, previously identified in culture filtrates of virulent Ptt isolates, using qPCR. Genes classified by InterPro as virulence factors, proteolytic, contributing to oxidation-reduction processes, or carbohydrate metabolic processes (CMP) including the cell wall degrading enzymes (CWDEs) had very high to extremely high expression levels. The most common temporal co-expression pattern, for 41 of the genes, was an upregulation from 24 h post inoculation (hpi) peaking at 96 hpi when necrotic symptoms became visible. The next most common pattern, for 27 of the genes, was also an upregulation from 24 hpi but peaking at 48 hpi. Genes categorised as encoding for CMP/CWDEs and involved in other metabolic processes were enriched in these patterns suggesting that the pathogen needs to access the plant tissue early in the interaction to access nutrients that can drive fungal growth. Other proteins with gene expression patterns that support a role for them in suppression of the plant defence response, particularly in the biotrophic stages of fungal growth included ceratoplatanin, LysM-like protein and proteins containing a CFEM-domain or a Jacalin-like domain. During the necrotrophic stage, gene expression was also upregulated for proteins possibly involved in toxin production, such as isoamyl alcohol oxidase and FAD-binding domain proteins. This is the first study monitoring fungal gene expression on a large scale during the interaction between barley and the NFNB disease pathogen Pyrenophora teres f. teres, highlighting candidates for future functional analysis.