Development of two multiplex PCR assays targeting improvement of bread-making and noodle qualities in common wheat

Wheat quality properties are genetically determined by the compositions of high and low molecular weight glutenin subunits, grain hardness, polyphenol oxidase (PPO) activity and starch viscosity. Two multiplex PCR assays were developed and validated using 70 cultivars and advanced lines from Chinese autumn-sown wheat regions. Multiplex PCR I includes molecular markers for genes/loci ω-secalin, Glu-B1-2a (By8), Glu-D1-1d (Dx5), Glu-A3d, Glu-B3 (for non-1B·1R type) and Pinb-D1b targeting improved gluten parameters and pan bread quality. Multiplex PCR II comprises markers for genes/loci Ppo-A1, Ppo-D1 and Wx-B1b targeting improved noodle quality. The results were consistent with those achieved by SDS-PAGE and RP-HPLC, indicating that the two multiplex assays were highly effective, with good repeatability and low costs enabling their use in wheat breeding programmes. In total, nine alleles (subunits) at locus Glu-B1, four at Glu-D1 and five at Glu-A3 locus were identified, and the alleles (subunits) Glu-B1b (7 + 8), Glu-B1c (7 + 9), Glu-D1a (2 + 12), Glu-D1d (5 + 10), Glu-A3a, Glu-A3c and Glu-A3d were most frequently present in the cultivars and lines tested. The 1B·1R translocation was present in 28 (40.0%) lines, whereas the Wx-B1 null allele for better noodle quality was present in only seven (10.0%) cultivars and advanced lines, and 37 (52.9%) lines had Pinb-D1b associated with hard grains. The allele Ppo-A1b on chromosome 2AL associated with lower PPO activity was present in 38 (54.3%) genotypes, whereas the less effective allele Ppo-D1a on chromosome 2DL, also associated with low PPO activity was present in 45 (64.3%) of genotypes. These two multiplex PCR assays should be effective in marker assisted selection targeting improved pan bread-making and noodle qualities.