Genome-Wide Association Study Reveals Key SNP Markers for Agro-Physiological Traits in Bread Wheat (Triticum aestivum L.)

Background : A genome-wide association scan (GWAS) is a powerful tool for identifying genetic variants and specific loci underlying complex traits. Bread Wheat ( Triticum aestivum L.) is one of the primary food resources in the world, and understanding its physiological parameters will help improve agronomic and yield traits. This study investigated single-nucleotide polymorphism (SNP) markers associated with physiological and agronomic traits in bread wheat to inform breeding programs. A diverse panel of 272 bread wheat genotypes was evaluated across two growing seasons (2019–2021) using a 16 × 17 rectangular lattice design with two replications. Key physiological traits, including carbon dioxide exchange and chlorophyll content, and agronomic traits, such as days to heading, days to maturity, flag leaf length, plant height, grain number per spike, grain weight per plant, thousand-grain weight, biological yield, and harvest index, were measured. Genotyping was conducted using a 90K SNP array at Trait-Genetics, Germany, yielding 17,093 high-quality SNPs after filtering for minor allele frequency and missing data (>10%). Results: Population structure analysis grouped the genotypes into five subgroups based on their genetic variation. GWAS was performed using General Linear Model (GLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Mixed Linear Model (MLM), identifying 320, 302, and 27 significant marker-trait associations (MTAs), respectively. Sixteen MTAs were consistently significant across models, including four stable MTAs detected in two cropping seasons. These MTAs harbored 139 high-confidence genes associated with nine traits. Conclusions: These findings provide valuable insights into the genetic architecture of key wheat traits, facilitating targeted breeding strategies to enhance yield.