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

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, <i>Kasp-SSV-1AS</i>, <i>Kasp-SSV-4AL</i>, <i>Kasp-TW-1AL</i>, <i>Kasp-TW-7BL</i>, and <i>Kasp-WAR-1AL</i>, 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.