To develop wheat varieties that meet the increasing global demand for food, wheat breeders are faced with the challenge of accumulating superior alleles for economically important agronomic traits, durable disease resistance, and high grain quality into a coupling configuration. Marker-assisted gene pyramiding provides the opportunity to develop cultivars, guided by genomic information, by assembling genetic regions of the desirable traits more precisely, quickly, and effectively. A doubled haploid population of 180 lines from the cross between Carberry and Vesper (registered CWRS varieties) was grown in replicated trials at different sites in the provinces of Saskatchewan and Manitoba from 2015 to 2017. Agronomic traits assessed included grain yield, thousand kernel weight, plant height, maturity, and lodging. From 2015 to 2018, the population was evaluated for resistance to Fusarium head blight (FHB) incidence and severity in corn spawn inoculated nurseries near Morden and Brandon (MB). Fusarium damaged kernels (FDK) and deoxynivalenol content (DON)were evaluated in 2015 and 2017. To determine grain quality, milling quality and rheology traits were assessed. A linkage map of 6157 SNP (Infinium iSelect 90k SNP wheat array) markers was used to perform quantitative trait locus (QTL) analysis. Several QTL were identified on 14 different chromosomes associated with the different measured traits. Agronomic traits were conditioned by genomic regions on chromosomes 2B, 4B, and 7D. QTL for quality traits were identified on chromosomes 1A, 1D, 2B, 2D, 3A, 4A, 4B, 5A, 5B,6B, and for FHB and its components on chromosomes 1A, 2B, 3A, 3B, 4B, 5A, 6B, and 7D. Complex genomic regions were identified on chromosomes 1A, 2D, and 4B. For example on 1A, favourable alleles for protein content, gluten strength, test weight, resistance to FHB symptoms and DON content were contributed by Carberry while the predicted water absorption favourable alleles were contributed by Vesper. Similarly, alleles in repulsion were observed in 2Dlocus, indeed dough extensibility favourable alleles were contributed by Carberry whereas Vesper contributed favourable alleles for gluten strength and test weight. On 4B chromosome, Carberry contributed favourable alleles for grain yield, resistance to lodging, and reduced plant height while Vesper contributed favourable alleles for lower DON content, FDK, protein, and test weight. These results highlight the difficulties that breeders encounter to develop wheat varieties that suit both farmers’ and millers’ needs. Multiple breeding approaches are needed to harness wheat genetic diversity and achieve favourable genes combinations within and among complex loci.