This study investigates the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) using genome-wide association studies (GWAS). The researchers evaluated 198 wheat germplasm lines for their seedling characteristics under controlled and drought stress conditions. Drought stress significantly reduced all seedling traits, with the maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain deeper insights, the researchers conducted a GWAS using 12,511 single nucleotide polymorphisms (SNPs), identifying 39 marker-trait associations (MTAs). Among these, 13 MTAs accounted for more than 10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were used to extract 216 candidate gene (CG) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with relevance to drought stress, encoding proteins such as WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, protein kinase domain, cytochrome P450, leucine-rich repeat domain superfamily, BURP domain, calmodulin-binding protein60, and ubiquitin-like domain. The findings provide valuable information for developing drought-resistant wheat varieties through marker-assisted breeding.This study investigates the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) using genome-wide association studies (GWAS). The researchers evaluated 198 wheat germplasm lines for their seedling characteristics under controlled and drought stress conditions. Drought stress significantly reduced all seedling traits, with the maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain deeper insights, the researchers conducted a GWAS using 12,511 single nucleotide polymorphisms (SNPs), identifying 39 marker-trait associations (MTAs). Among these, 13 MTAs accounted for more than 10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were used to extract 216 candidate gene (CG) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with relevance to drought stress, encoding proteins such as WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, protein kinase domain, cytochrome P450, leucine-rich repeat domain superfamily, BURP domain, calmodulin-binding protein60, and ubiquitin-like domain. The findings provide valuable information for developing drought-resistant wheat varieties through marker-assisted breeding.