Fhb1 (Qfhs.ndsu-3BS) is the most important quantitative trait locus (QTL) conferring resistance against Fusarium head blight disease (FHB). Although this QTL has been extensively deployed in breeding programs worldwide, the presence of Fhb1 does not always guarantee strong resistance across different genetic backgrounds. Understanding the genetics of resistance has been impeded by uncertainty regarding the causal gene within the Fhb1 locus, and in durum, the underlying molecular mechanisms remain largely unexplored. To improve our understanding of FHB resistance in durum, we performed a transcriptomic analysis coupled with a haplotype study of six related durum lines in response to Fusarium graminearum using a novel reference genome, Sumai 3. These lines were derived from crosses between Sumai 3 and PI277012 cultivars, and represent lines with or without Fhb1, 5AS (Qfhb.rwg-5A.1) and 5AL (Qfhb.rwg-5A.2), showing varying levels of FHB resistance. Results revealed no significant change in the expression of the PFT gene within the Fhb1 locus, while TaHRC expression was observed only in lines with the Fhb1 QTL. However, the expression pattern of TaHRC did not support its role as the causal gene conferring resistance. Instead, results showed that the interaction of the Fhb1 locus with genes from 5A plays a key role in defining FHB resistance. Fusarium head blight susceptibility of lines carrying Fhb1 was further studied using haplotype analysis to understand how genes within each haploblock, inherited from respective parents, contribute to variations in FHB susceptibility or resistance. To further investigate gene expression dynamics, we will employ Quantitative Real-Time PCR and Enzymatic Methyl-seq assays.