Wheat (Triticum aestivum L.) is one of the most important crops consumed by humans around the world. Improving the end-use quality traits is one of the major objectives in wheat breeding programs. However, little is known about the genomic regions controlling these traits. Discovering the genetic architecture underlying important end-use quality traits can accelerate breeding via marker-assisted selection (MAS) in addition to providing genomic and biological information. Therefore, for this dissertation, a quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) were conducted to identify QTL for 16 end-use quality traits, including the grain protein content, flour extraction rate, eight mixograph-related parameters, and six baking-related properties. A population of 127 recombinant inbred lines (RILs) from a cross between Glenn (PI-639273) and Traverse (PI-642780) was developed for the QTL mapping study, and an association panel of 355 elite spring wheat lines was used for the GWAS study. The phenotyping of these traits was performed in nine environments in North Dakota, USA, over a three-year period. The genotyping for both the RIL population and association panel was conducted using the wheat Illumina iSelect 90K SNP assay. A total of 76 additive QTL (A-QTL) and 73 digenic epistatic QTL (DE-QTL) were found for the 16 end-use quality traits in the QTL mapping study. These QTL were distributed across all wheat chromosomes except chromosome 3D. Overall, 12 stable major A-QTL and three stable DE-QTL were identified for the end-use quality traits in the QTL mapping study, indicating that both A-QTL and DE-QTL played an important role in controlling end-use quality traits. In addition to the QTL mapping study, a total of 91 significant marker–trait associations (MTA) were identified for the end-use quality traits in the GWAS study. These MTA were distributed across all wheat chromosomes except chromosome 4D. Overall, the current study identified multiple novel stable QTL that could be used in MAS for end-use quality trait improvement in wheat breeding programs.