High-molecular-weight glutenin subunits (HMW-GSs) play a critical role in determining the viscoelastic properties of wheat.  As the organelle where proteins are stored, the development of protein bodies (PBs) reflects the status of protein synthesis and also affects grain quality to a great extent.  In this study, with special materials of four near-isogenic lines in a Yangmai 18 background we created, the effects of Glu-A1 and Glu-D1 loci deletions on the development and morphological properties of the protein body, protein components and dough properties were investigated.  The results showed that the deletion of the HMW-GS subunit delayed the development process of the PBs, and slowed the increases of volume and area of PBs from 10 days after anthesis (DAA) onwards.  In contrast, the areas of PBs at 25 DAA, the middle or late stage of endosperm development, showed no distinguishable differences among the four lines.  Compared to the wild type and single null type in Glu-A1, the ratios of HMW-GSs to low-molecular-weight glutenin subunits (LMW-GSs), glutenin macropolymer (GMP) content, mixograph parameters as well as extension parameters decreased in the single null type in Glu-D1 and double null type in Glu-A1 and Glu-D1, while the ratios of gliadins (Gli)/glutenins (Glu) in those types increased.  The absence of Glu-D1 subunits decreased both dough strength and extensibility significantly compared to the Glu-A1 deletion type.  These results provide a detailed description of the effect of HMW-GS deletion on PBs, protein traits and dough properties, and contribute to the utilization of Glu-D1 deletion germplasm in weak gluten wheat improvement for use in cookies, cakes and southern steamed bread in China and liquor processing.