The narrow genetic base in the current wheat germplasm stands up as a major challenge for both wheat yield and quality improvement. Aegilops tauschii, the wheat wild relative and the D genome donor, is a good source for developing biotic and abiotic stresses in arid regions and improving wheat yield and quality due to its enormous and limitedly exploited genetic diversity. This study used 392 multiple synthetic derivatives (MSD) panel developed by crossing and backcrossing the Japanese wheat cultivar ‘Norin 61’ and 43 different synthetic hexaploidy wheat lines. The synthetic hexaploidy lines were developed by crossing the tetraploid wheat cultivar ‘Langdon’ with 43 Ae. tauschii accessions represent the entire species range and cover its three lineages. Therefore, this MSD panel is an attractive platform to explore the genetic diversity of Ae. tauschii regarding quality traits in the background of a wheat cultivar. The objectives of this study are to explore allelic variation at the Glu-1, to evaluate dough strength, to know the relationship between protein content and grain yield, and to identify good flour quality lines. A broad diversity was observed for alleles at the Glu-D1 locus, reflecting the influence of the different chromosomal inserted segments from Ae. tauschii. A large variation was observed in dough strength even between lines with the same HMW-GS composition. We document an adverse effect of allele 5t+10t and a relatively positive effect of allele 2t+12.1t from Ae. tauschii on dough strength. We identified four superior lines that improved the flour quality. The regression between grain yield and protein content for MSD lines revealed no correlation between the two traits. We could identify MSD lines maintained comparable yields and high protein content compared to the backcrossed parent ‘Norin 61’. These MSD lines are promising and could serve as a good source to improve wheat flour quality without any concern about the deterioration in grain yields.