AbstractWheat stem rust disease caused byPuccinia graminisf. sp.tritici(Pgt) is a global threat to wheat production. Fast evolving populations ofPgtlimit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated withPgtinfection in susceptible and resistantTriticum aestivumgenotypes as well as the non-hostBrachypodium distachyon. We targeted our analysis to genes with differential expression inT. aestivumand genes suppressed or not affected inB. distachyonand report several processes potentially linked to susceptibility toPgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance toPgtthrough removal or modification of putative susceptibility genes.