Transcriptome analysis in the maize-Ustilago maydis interaction identifies maize-line-specific activity of fungal effectors

The biotrophic pathogen Ustilago maydis causes smut disease on maize (Zea mays) and induces the formation of tumours on all aerial parts of the plant. Unlike in other biotrophic interactions, no gene-for-gene interactions have been identified in the maize-U. maydis pathosystem. Thus, maize resistance to U. maydis is considered a polygenic, quantitative trait. Here, we study the molecular mechanisms of quantitative disease resistance (QDR) in maize, and how U. maydis interferes with its components. Based on quantitative scoring of disease symptoms in 26 maize lines, we performed an RNA-Seq analysis of six U. maydis-infected maize lines of highly distinct resistance levels. In accordance with the complex nature of QDR, the different maize lines showed specific responses of diverse cellular processes to U. maydis infection. On the pathogen side, our analysis identified 406 U. maydis genes being differentially expressed between maize lines, of which 102 encode predicted effector proteins. Based on this analysis, we generated U. maydis CRISPR/Cas9 knockout mutants for selected candidate effector sets. Infections of different maize lines with the fungal mutants and subsequent RNA-sequencing identified effectors with quantitative, maize-line-specific virulence functions, and revealed auxin-related processes as a possible target for one of them. Thus, we show that both transcriptional activity and virulence function of fungal effector genes are modified according to the infected maize line, providing new insights into the molecular mechanisms underlying QDR in the maize-U. maydis interaction.