Development, Evaluation, and Application of a Molecular Marker System for Wheat Quality Breeding in China

To address the limitations of traditional wheat quality breeding, this study developed a Wheat Quality Molecular Marker Selection System (QMMS) by integrating key genetic loci controlling core quality traits: grain protein content (GPC), grain hardness (GH), and high-molecular-weight glutenin subunits (HMW-GS). The QMMS comprises three KASP markers (Kgpc-2B, Kgpc-2D, Kgpc-4A) and two duplex KASP (dKASP) markers (Pin-ab, Glu-AD), enabling cost-effective (≈5 CNY per sample) and high-throughput genotyping. Systematic validation was conducted using four panels of materials: representative varieties, breeding nursery materials, regional trial materials from the Middle and Lower Reaches of the Yangtze River, and advanced lines from four cooperative institutions. Results showed that (1) the QMMS accurately distinguished quality types of representative varieties: strong-gluten varieties carried five or more strong-gluten–favorable alleles, while weak-gluten varieties harbored five or more weak-gluten favorable alleles; (2) in breeding nursery materials, quality traits increased significantly with the number of aggregated strong-gluten favorable alleles, and 48.15% of strong-gluten candidates met strong- and medium-strong-gluten standards; (3) in regional trial materials, 15.25% (36/236) and 1.69% (4/236) of lines carried ≥5 strong-gluten and weak-gluten favorable alleles, with low utilization of Kgpc-2D and Pina/Pinb favorable alleles (<30%); and (4) the QMMS screened 273 strong-gluten and 27 weak-gluten candidates for cooperative institutions, matching their breeding focuses. In conclusion, the QMMS provides reliable technical support for precise and efficient wheat quality breeding.