From Bioinformatics to Identifying R-genes, Enhancers, Signaling Pathways and Pathogen Elicitors in the Barley-Stem Rust Pathosystem

• Main Author: Sharma Poudel, Roshan
• Format: Others
• Published: North Dakota State University 2018
• Online Access: https://hdl.handle.net/10365/27946

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is a threat to wheat and barley. Rpg1 is the only deployed stem rust resistance gene in barley that provides resistance to the predominant races in North America, except to the local race QCCJB and the widely virulent race TTKSK (aka Ug99) and its lineages. The barley rpg4-mediated resistance locus (RMRL) confers resistance against the majority of Pgt races, including TTKSK and its lineage. With the goal of identifying Pgt effectors/suppressors that elicit/suppress RMRL resistance responses twenty-four Pgt isolates showing differential infection types were genotyped utilizing in planta RNAseq. The RNAseq experiment identified 114K SNPs within genes that resulted in predicted nonsynonymous amino acid changes and were utilized to identify genes associated with virulence/avirulence. Twenty-two genes were identified that were associated with RMRL virulence that represent candidate suppressors of resistance. Host differential gene expression analysis comparing virulent vs avirulent isolates identified virulent isolate specific down regulation of stress response genes, genes involved in chloroplastic ROS, and non-host resistance responses, suggesting that Pgt isolates may contain a conserved virulence factor that elicits RMRL responses and virulent isolates contain suppressors of virulence rather than dominant avirulence genes. The second chapter focused on the observations that introgression of RMRL into the elite malting variety Pinnacle (Rpg1+) resulted in susceptibility to Pgt race QCCJB (RMRL) and HKHJC (Rpg1) suggesting the presence of a gene required for rpg4/Rpg5 and Rpg1 resistance. Utilizing a Pinnacle RMRL-NIL X Q21861 derived RIL population and PCR-GBS genotyping, the required for rpg4- and Rpg1-mediated resistance 1, Rrr1 gene was mapped ~5cM proximal to RMRL on barley chromosome 5H. A second gene required for Rpg1- mediated resistance 2, Rrr2, complimentary to Rrr1 was mapped to the telomeric region of the short arm of barley chromosome 7H. A novel Pgt race TTKSK resistance gene designated RpgHv645 was identified in an unimproved swiss landrace Hv645. Utilizing a RIL population developed from a Hv645 X Harrington cross and Pgt race TTKSK phenotyping data generated at the adult plant stage in Njoro, Kenya, RpgHv645 was mapped distal of RMRL and delimited to an ~11cM region. === National Science Foundation (NSF) CAREER grant No. 1253987