Genome‐wide association analyses reveal loci controlling 1000‐kernel weight, harvest index, biological yield, and grain yield in bread wheat

Abstract Understanding the genetic basis of grain yield and related traits in bread wheat under different water regimes is essential for improving moisture stress tolerance and water‐use efficiency. This study aimed to identify stable loci associated with these traits under rainfed conditions. A single‐nucleotide polymorphism (SNP)‐based multi‐locus genome‐wide association study (ML‐GWAS) was conducted using 22,962 polymorphic SNPs and six ML‐GWAS models in 220 bread wheat genotypes sourced from International Maize and Wheat Improvement Center, International Center for Agricultural Research in the Dry Areas, and Ethiopian breeding programs. Field trials were carried out across three environments using an alpha lattice design with two replications. Combined analysis revealed highly significant ( p < 0.001) differences among genotypes for most traits. The ML‐GWAS identified seven stable quantitative trait nucleotides (QTNs) associated with four yield and yield‐related traits, spanning 21 chromosomes. Candidate genes near these QTNs encode key functional proteins, including serine‐rich protein, TF‐B3 domain protein, zinc finger GRF‐type protein, protein kinase domain protein, glycoside hydrolase family five proteins, cytochrome P450, polycomb VEFS‐box protein, and auxin response factor implicated in drought tolerance, nutrient remobilization, and developmental regulation. These results provide valuable genomic resources for future breeding programs, offering robust markers for marker‐assisted and genomic selection to accelerate the development of wheat varieties with improved resilience and yield stability under rainfed conditions.