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

Abstract

The biotrophic pathogen 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 Ustilago maydis is considered a polygenic, quantitative trait. Here, we study the molecular mechanisms of quantitative disease resistance (QDR) in maize, and how Ustilago maydis interferes with its components. Based on quantitative scoring of disease symptoms in 26 maize lines, we performed an RNA-Seq analysis of six Ustilago 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 Ustilago maydis infection. On the pathogen side, our analysis identified 406 Ustilago maydis genes being differentially expressed between maize lines, of which 102 encode predicted effector proteins. Based on this analysis, we generated Ustilago 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-Ustilago maydis interaction.

Effectors with Different Gears: Divergence of Ustilago maydis Effector Genes Is Associated with Their Temporal Expression Pattern during Plant Infection

“…For instance, the U. maydis effector Apathogenic in B73 (ApB73) is necessary for the infection of maize line B73, whereas the maize line Early Golden Bantam could be infected, although with lower virulence, when apB73 was deleted [ 11 ]. Similarly, U. maydis effector UMAG_02297 contributes to full virulence in maize line CML322 but not in Early Golden Bantam [ 12 ]. Conceivably, differences in nature and function of effectors in the pathogen life cycle must impact their mutability.…”

High-quality genome assembly of Verticillium dahliae VD991 allows for screening and validation of pathogenic genes

“…Gene ontology (Ashburner et al, 2000) and KEGG (Kanehisa et al, 2004) enrichment analyses were performed using the R-package "clusterProfiler". In addition, a weighted gene co-expression network analysis (WGCNA) was performed using the R package "WGCNA" (Langfelder and Horvath, 2008;Duan et al, 2022), with the FPKM values as input, as described previously (Schurack et al, 2021).…”

Effectors with different gears: divergence ofUstilago maydiseffector genes is associated with their temporal expression pattern during plant infection

“…The copyright holder for this preprint this version posted December 11, 2020. ; https://doi.org/10.1101/2020.12.10.419192 doi: bioRxiv preprint line CML322 but not in Early Golden Bantam [12]. Conceivably, differences in nature and function of effectors in the pathogen life cycle must impact their mutability.…”