Wheat quality is an important target trait. Previous studies mainly focus on storage protein, but their contribution to quality is partial, and most loci for quality are still undetected. Wild species of wheat are valuable resources for wheat improvement and introgression lines (ILs) are the ideal materials for detecting quantitative trait loci (QTL). In this study, a set of 82 BC5 F2-6 ILs, carrying a range of introgressed chromosome segments from a synthetic hexaploid wheat Am3 (Triticum carthlicum x Aegilops tauschii), was developed and genotyped with 170 microsatellite markers. QTL analysis was performed for 14 parameters, sodium dodecyl sulfate sedimentation volume, grain protein content (GPC), grain hardness and 11 mixograph parameters, associated with end-use quality of wheat, using the materials harvested in three environments. This led to the detection of 116 QTL, with c. 95% of the positive alleles contributed by Am3. Six important and novel genomic regions for bread-making quality were found on chromosomes 2D, 3A, 4A, 4B, 5A and 6A. These loci for bread-making quality showed pleiotropy and had large positive effects on several quality parameters with no or very weak negative effect on grain yield, thus demonstrating the value of synthetic wheat as a source of useful genetic variation for the improvement of bread wheat quality.
