Fusarium head blight (FHB) incited by Fusarium graminearum, is currently the most devastating disease of barley (Hordeum vulgare L.) in western Canada. Type B trichothecene mycotoxins e.g. deoxynivalenol (DON) associated with FHB are closely monitored by both malting and livestock feed industries. Breeding disease-resistant varieties is a sustainable disease management practice, however, this is complicated by quantitative-based resistance. To date, breeding efforts have largely relied on labour-intensive screening nurseries. Two studies focus on the evaluation of a single nucleotide polymorphic (SNP) marker array (Barley 50K SNP) in i) genome-wide association study (GWAS); ii) genomic estimated breeding values (GEBV) whole-genome marker prediction. While GWAS identified numerous genomic associations with FHB and DON, they generally were small effects explaining a low proportion of the phenotypic variance. Genomic estimated breeding values (GEBVs) were calculated by classical statistical and machine learning approaches, where both were able to demonstrate moderate prediction is possible for FHB and DON content. Genomic selection is thus recommended as an efficient breeding approach vs. considerations of individual SNP markers. The F. graminearum population of western Canada has shifted towards 3-acetyl-deoxynivalenol (3ADON)-producers, which tend to accumulate higher levels of DON. In vitro selection (IVS) has been successfully used to identify resistant somaclonal variants. Another study involves poly-A RNA-sequencing contrast of IVS derived variety Norman vs. its parent, CDC Kendall. Different transcriptional alternations were detected in response to infection by 3ADON, 15ADON, and nivalenol (NIV) – producing strains of F. graminearum. In the final experiment, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to evaluate mycotoxin composition in rachis and grains for a group of field-inoculated varieties with differential resistance levels. The conjugate form deoxynivalenol-3-glucoside (DON3G) was found to occur at a significant level (26%) of total toxins. While varieties differed in DON content, the ratio of DON3G/DON appeared stable across genotypes. In summary, the dissertation contributed to novel research through the identification of feasible genomics-based breeding strategies for developing FHB resistance and lowering DON, contributed to an understanding of IVS resistance of Norman, identified gene targets of differentially expressed genes between the varieties, and has identified toxin-conjugation as a resistance factor.