Genome-wide association analysis identifies SNP loci for multi-stage yield-related traits in wheat

Introduction Wheat is a major global food crop, and improving its yield is essential for food security. Identifying genetic loci and candidate genes associated with yield-related traits is crucial for molecular breeding. Methods A panel of 768 common wheat varieties from domestic and international sources was evaluated over two consecutive years (2024 and 2025) in Tai’an. Three growth-stage traits, eight agronomic traits, and three seedling-stage traits, including root length, seedling weight, and seedling height, were measured. Genotyping was performed using a 55K SNP array, and a genome-wide association study was conducted using a linear mixed model. Results Population structure and kinship analyses classified the varieties into primitive landraces and modern cultivars. A total of 49,768 high-quality SNPs were identified, covering 82.73% of the genome with an average marker density of 0.29 Mb. Among them, 17,293, 18,313, and 14,162 SNPs were located on the A, B, and D subgenomes, respectively. Association analysis revealed 544 SNP loci significantly associated with yield-related traits across 21 chromosomes, of which 49 were consistently detected in both years. Additionally, 60 loci were associated with two or more traits, indicating potential pleiotropic effects, and were distributed on 16 chromosomes (excluding 3D, 4B, 4D, 7A, and 7B). Discussion This study identifies SNP markers associated with key traits across growth stages in common wheat and provides a basis for the discovery of candidate genes and favorable alleles. These findings may facilitate the utilization of elite genetic resources for yield improvement in wheat breeding.