To carry out wheat breeding programs, proteins were identified and quantified (through sodium dodecyl sulfate polyacrylamide gel electrophoresis [SDS‐PAGE] and size‐exclusion high‐performance liquid chromatography [SE‐HPLC]) and six allele‐specific markers were tested on 45 Brazilian cultivars. A microscale baking test was applied to associate analytical and genetic responses with baking quality. The results suggested a prevalence of the subunits 2* and 1 in chromosome 1A; 7+8, 7+9, and 17+18 in 1B; and 5+10 in 1D; absence of 1BL/1RS translocation in 62.2% of the genotypes; and presence of Pinb‐D1b and Glu‐A3d in 8.9% of the genotypes. The average SE‐HPLC values were 37.50 and 45.42% for polymeric protein in total protein (PPP) and unextractable polymeric protein (UPP), respectively, and 1.29 for the gliadin‐to‐glutenin (GLI/GLU) ratio, with significant variation among the genotypes (P ≤ 0.05). The baking test also showed a significant difference (P ≤ 0.05) between the cultivars under the same conditions. The cultivars without the 1BL/1RS translocation with rye also showed better results for UPP, PPP, and GLI/GLU in relation to those possessing translocation. These results corroborate for selection of HMW subunits 5+10, cultivars without translocation with rye, with high UPP values and a balanced GLI/GLU ratio (around 1.0) with the objective of obtaining greater wheat baking quality.