Genetical Genomic Dissection of Stem Rust Infection in Barley.

To identify breeding and biochemical targets that will mitigate a stem rust epidemic currently threatening barley and wheat crops worldwide, we have performed QTL and eQTL mapping experiments to connect genetic loci that confer stem rust resistance with gene expression networks that are responsive to infection.  Barley1 GeneChips have been used to profile the transcriptome of inoculated and mock-inoculated leaves of Q21861, SM89010, and seventy-five Q21861 x SM89010 doubled haploid lines that vary both qualitatively and quantitatively in their reaction to Puccinia graminis f. sp. tritici (Pgt), race TTKS, commonly called Ug99.  The linkage map of the QSM population was built using Single Feature Polymorphism (SFP) markers derived from our GeneChip hybridizations.  These were placed onto a skeletal map initially populated by markers with coincident occurrence in the Steptoe x Morex doubled haploid SFP map (Potokina et al. 2008, Plant Journal 53:90-101).  Our eQTL analyses thus far have focused on probesets that show differential expression between inoculated and mock-inoculated leaves, allowing identification of loci that regulate the genes and gene networks most relevant to disease defense.  These analyses have revealed three novel phenomena that typify the inheritance of gene expression in Pgt TTKS-barley interactions.  First, an eQTL hotspot was not found at the rpg4/Rpg5 locus which mediates qualitative resistance to Pgt TTKS.  Second, in mock-inoculated tissue, >800 genes are regulated by two major eQTL hotspots 2H, bin40 and chromosome 6H, bin55.  Lastly, at 24 hours after inoculation, an oversampled fraction of these 800 genes collectively show a significant differential response to infection and their primary regulation is transferred to a new loosely linked locus on chromosome 2H, bins 20 to 25.  These loci represent candidates for master regulators that reprogram the host transcriptome in response to Pgt TTKS.