Lihua Liu

In this study, we report the development of the high-quality BAAFS Wheat 90 K SNP array for molecular characterization of wheat cultivars, and systematically validate its utility for identifying genetic loci underlying wheat processing quality traits. This optimized array incorporates high-quality SNP markers derived from the Illumina Wheat 90 K iSelect SNP array and the Axiom ^® Wheat 660 K SNP array, resulting in a final set of 84,661 loci. Among these loci, 79 represent gene-specific functional markers, and all loci are precisely anchored to the Chinese Spring (CS) telomere-to-telomere (T2T) reference genome, guaranteeing high genomic positional accuracy. These 84,661 loci show uneven distribution across the A (37.9%), B (42.5%), and D (18.0%) subgenomes, with 46.91% of the loci localized within genic regions. Genotyping was conducted on 190 accessions and 200 F ₂ individuals derived from the cross between Shaanxibaimai and L43, generating 91.0% and 71.0% high-qualitymarkers, respectively. A total of 1041 Chinese wheat cultivars representing eight major agro-ecological zones were genotyped. Principal component analysis (PCA) showed that the first two principal components collectively explained 12.4% of the total genetic variance. 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 90 K 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.

Molecular characterization of wheat varieties is of high importance for wheat breeding. In the present study, 1883 Chinese wheat cultivars released between 1971 and 2025 were genotyped using a wheat 90K SNP array. Analysis of genetic diversity indicated a consistent A > B > D pattern, with the D subgenome showing the lowest genetic diversity and fastest LD decay (4.2 Mb), indicating diminished genetic diversity driven by breeding and selection. Population structure analysis revealed ten genetic clusters with clear ecological preferences, whereas genetic differentiation was weak (FST < 0.05) and gene flow extensive (Nem > 1), indicating the co-existence of strong ecological adaptation and frequent interregional germplasm exchange. Selective sweeps were identified on chromosome 5A (TaVRN1) and 2D (Rht8/RNHL-D1) regions controlling vernalization, plant height, and stress tolerance. Despite high gene flow, these loci for variety adaptiveness remained differentiated, highlighting the impact of artificial selection. Average pairwise genetic similarity was 0.56, but only a minority of cultivar pairs exceeded 0.98, especially in the Northeastern Spring Wheat and Middle-Lower Yangtze River Facultative Wheat regions, revealing severe genetic homogeneity from the excessive use of core parents. Nucleotide diversity increased to a peak in 2011–2015. These findings indicate that Chinese wheat cultivars still harbor significant potential for genetic improvement, highlighting the critical need to integrate exotic germplasm into core breeding parents to drive future advancements.