Knowledge and understanding of the genetic basis and map relationship of agronomic, disease resistance and end-use quality traits assists in crop breeding of new varieties. Although genes governing various traits of wheat (Triticum aestivum L.) have been dissected by molecular mapping studies, many remain unidentified and the interactions between genes/loci are poorly understood. The objective of this study was to investigate and identify loci associated with economically important agronomic, disease resistance and end-use quality traits in two Canadian spring wheat varieties. A doubled haploid (DH) population comprising 204 lines was developed from a cross of CDC Hughes/AAC Concord. During growing season 2015/16, 137 lines of the population were planted near Irwell, New Zealand and subsequently spring 2016 near Swift Current, SK, and Brandon, MB. A total of 204 lines including those from 2016 were planted in replicated yield plots near Swift Current in 2017 and 2018. Additionally in 2018 the population was planted near Lethbridge, AB in stripe rust nursery, and Brandon, MB and Morden, MB in Fusarium head blight (FHB) nurseries. Data on plant height, lodging, maturity, hectolitre weight, kernel weight and grain yield were collected near Swift Current. Grain protein, flour milling yield, predicted dough water absorption and rheology traits were analysed using grain harvested from Swift Current trials. Stripe rust infection was scored near Swift Current in 2016 and Lethbridge in 2018, and FHB near Brandon in 2016 and 2018 and Morden in 2018. Main stems of the lines were rated for stem solidness at maturity near Irwell, New Zealand in 2016 and near Swift Current, SK 2016 in 2017 and 2018. The population was genotyped with the 90K SNP array. A high density map was generated using MSTMap software and QTL analysis performed using MapQTL6. QTL associated with multiple agronomic, disease resistance and/or quality traits were identified on chromosomes 1A, 2D, 4A, 4B, 5A, 5B and 6B, and single traits on 2B, 3D and 7D. Considering no pleiotropy was in action, the desirable alleles associated with some of the traits of interest were in repulsion phase with each other. These results emphasise the difficulties faced in wheat variety development and confirm the need to utilize diverse breeding strategies to achieve breeding objectives even when genetic diversity of parents is low.