Development of a high-quality 90 K SNP array and its application in mining genes associated with wheat processing quality traits

In this study, we report the development of a high-quality BAAFS Wheat 90K SNP array for the molecular characterization of wheat cultivars and systematically validated its efficacy in identifying genetic loci associated with wheat processing quality traits. This optimized array integrates high-quality SNP markers from the Illumina Wheat 90K iSelect SNP array and the Axiom® Wheat 660K SNP array, yielding a total of 84,661 loci. Among these loci, 79 are gene-specific functional markers and all loci are precisely anchored to the Chinese Spring (CS) telomere-to-telomere (T2T) reference genome, ensuring high genomic positional accuracy. The 84,661 loci are unevenly distributed across the A (37.9%), B (42.5%), and D (18.0%) subgenomes, with 46.91% of the loci localized within genic regions—an attribute that enhances the array’s utility for functional genetic analysis. Genotyping was performed on 190 wheat cultivars and 200 F 2 individuals derived from the cross between Shaanxibaimai and L43, generating high-quality genotypic data with marker call rates of 91.0% and 71.0%, respectively. A total of 1,041 Chinese wheat cultivars representing eight major agro-ecological zones were genotyped, and model-based clustering analysis resolved these cultivars into eight distinct subpopulations, with pairwise fixation index (Fst) values ranging from 0.265 to 0.503. Principal component analysis (PCA) showed that the first three principal components collectively explained 17.07% of the total genetic variance. Additionally, 2,478 recombination hotspots were identified, and these hotspots were predominantly concentrated near chromosomal termini. Genome-wide association studies (GWAS) were conducted by integrating phenotypic data of seven processing quality traits from Value for Cultivation and Use (VCU) trials, including dough stability time, dough development time, maximum resistance, extension area, grain texture, water absorption, and hardness index. A total of 294 significant marker-trait associations (MTAs) were detected, corresponding to 62 QTLs associated with these processing quality traits, and a pleiotropic region on chromosome 1D (408–423 Mb) was identified to regulate multiple dough-quality traits, explaining 7.18–31.56% of the phenotypic variance. Another key locus on chromosome 5D (2.7–7.0 Mb) was associated with grain hardness and texture, accounting for 0.11–16.53% of phenotypic variation. Novel QTLs, distinct from previously reported loci, were identified on chromosomes 3D (associated with dough development time and maximum resistance), 5A (associated with grain texture), and 6D (associated with water absorption). Candidate gene analysis was further performed for these three novel QTLs, and the pleiotropic QTL QDDT/DST/MR/EA.baaf-3D was found to explain 12.39–27.08% of the phenotypic variation for dough-related traits, highlighting its potential value for wheat quality improvement. To facilitate efficient marker-assisted selection (MAS) in wheat breeding, four Kompetitive Allele-Specific PCR (KASP) markers were successfully developed for key loci associated with processing quality traits. Collectively, the BAAFS Wheat 90K SNP array provides a cost-effective, high-fidelity genomic tool for wheat genetic research and breeding applications, including germplasm evaluation, genetic mapping, variety identification, precision breeding, MAS, and genomic selection (GS), with particular utility for dissecting the genetic basis of wheat processing quality and accelerating the genetic improvement of critical agronomic traits.