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 as effectors by silencing complementary host genes. Meanwhile, various wheat-derived sRNA sequences are induced or repressed upon infection, yet their targets and functions 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. Like other RNAi-equipped fungi, P. striiformis produces thousands of 20–22 nt sequences with a preference for uracil at the 5′ position. We observed precise post-transcriptional processing and high accumulation of specific sRNA sequences. Some predicted precursors possess a microRNA-like stem-loop secondary structure; others originate from much longer inverted repeats containing gene sequences. Target transcripts were identified by the observation of high slicing frequency at the precise position of sRNA binding sites. Targets among fungal transcripts indicate endogenous regulation of fungal development; wheat target transcripts indicate cross-kingdom gene silencing. Some wheat targets, but not all, are reduced in expression during infection with stripe rust, suggesting a complex pattern of gene induction and repression. Analysis of wheat miRNA loci revealed novel candidate MIR genes in each of the three wheat subgenomes. Resistant and susceptible host cultivars showed differential expression of miRNAs involved in the regulation of disease resistance and phosphate uptake genes. This work highlights the small RNA repertoire of an important plant pathogen, as well as the sRNA-mediated responses of its host. The target genes identified will provide useful prospects for the development of pathogen control biotechnology.
|Advisor:||Hulbert, Scot H|
|Commitee:||Neff, Michael M, Okubara, Patricia A, See, Deven R|
|School:||Washington State University|
|Department:||Molecular Plant Sciences|
|School Location:||United States -- Washington|
|Source:||DAI-B 81/9(E), Dissertation Abstracts International|
|Subjects:||Plant sciences, Agriculture, Bioinformatics|
|Keywords:||Fungi, Genomics, MicroRNA, Plant pathology, Small RNA, Wheat|
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