Uncover the genetic basis of processing quality related traits in common wheat (Triticum aestivum L.) using genome-wide association mapping

Introduction Improving wheat processing quality is one of the primary objectives in modern wheat breeding. Among various wheat quality parameters, SDS sedimentation volume (SSV), test weight (TW), and water absorption rate (WAR), significantly influence end-use flour quality. The Huang-Huai Winter Wheat Region (HHWWR) is the largest commercial wheat production region in China, making the breeding of high-quality wheat varieties adapted to this region particularly important. Methods In this study, genome-wide association study (GWAS) analysis for grain quality traits were conducted based on 310 wheat varieties collected from HHWWR. The SSV, TW, and WAR were evaluated at Anyang of Henan and Yangling of Shaanxi at the 2022–2023 and 2023–2024 cropping seasons. Results and discussion Totally, three stable SSV related loci were detected on chromosomes 1A and 4A, explaining 7.2-9.2% of the phenotypic variation (PVE). Seven stable TW loci were distributed on chromosomes 1A, 1B, 4A, 5A, 6D, and 7B, with PVE ranging from 7.0% to 20.1%. In addition, 5 stable WAR-related loci were found on chromosomes 1A, 3B, 4B, and 4D, and accounting for 7.0-8.7% of PVE. Among these, 5 loci co-localized with known genes or loci, whereas the remaining 10 loci are potentially novel. We further identified several candidate genes involved in various biological pathways in plants, including growth and development, stress responses, metabolic regulation, and signal transduction. Moreover, five Kompetitive Allele-Specific PCR (KASP) markers, Kasp-SSV-1AS , Kasp-SSV-4AL , Kasp-TW-1AL , Kasp-TW-7BL , and Kasp-WAR-1AL , were developed and validated in 123 common wheat accessions. This study provides stable loci and validated KASP markers, thereby paving the way for the molecular improvement of wheat quality through marker-assisted breeding.