Small RNA-mediated gene regulation on both sides of the wheat stripe rust interaction

Primary author: Nicholas Mueth

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman


Wheat stripe rust is a global disease that burdens farmers with yield loss and increased fungicide expenses. The causative agent, the fungus Puccinia striiformis f. sp. tritici, develops infection structures inside living plant cells, suppressing the defense response in order to steal nutrients for further growth and reproduction. While many fungal virulence-promoting factors are proteins, it was recently discovered that small RNA molecules also function in this manner by silencing complementary host genes. Meanwhile, wheat-derived small RNAs are induced or repressed during infection, yet their targets are mostly unknown. In this work, small RNA, degraded RNA, and gene expression data were combined to investigate post-transcriptional gene regulation on both sides of the host-parasite interaction. Our goal was to identify target transcripts by the observation of high transcript slicing frequency at the precise position of small RNA binding sites. Targets among fungal transcripts indicated native regulation of fungal development; wheat target transcripts indicated cross-kingdom gene silencing. Some wheat targets, but not all, showed reduced expression during infection with stripe rust, suggesting a complex pattern of gene induction and repression. Analysis of wheat microRNA loci revealed novel candidate genes in each of the three wheat subgenomes. Resistant and susceptible wheat varieties showed differential expression of microRNAs involved in the regulation of disease resistance and phosphate uptake. This work highlights the small RNA repertoire of an important plant pathogen, as well as the responses of its host. The newly-identified target genes will provide prospects for the development of pathogen control biotechnology.