Drought stress at all stages affects physiological and morphological characteristics important for wheat growth and development. Two types of population, i.e., International Triticeae Mapping Initiative (ITMI) and Synthetic derivatives (SYN-DER) were utilized to study the effects of drought stress in wheat. 209 recombinant inbred lines of ITMI, derived from synthetic wheat (W7984) x Opata, were evaluated at seedling stage for quantitative trait loci (QTL) identification. Our results indicated moderate to high broad sense heritability (H) among the RILs population with significant differences (p<0.01) revealed by analysis of variance (ANOVA). A high-density linkage map was constructed with 2639 genotyping-by-sequencing (GBS) markers that covered 5047 cM with an average marker density of 1.9 cM/marker. 16 QTLs were identified by composite interval mapping (CIM), distributed over nine chromosomes, out of which 10 QTLs were identified under water-limited (WL) conditions and 6 were identified under well-watered (WW) conditions with 4 to 59% of the phenotypic variance. In addition, 216 accessions of synthetic wheat germplasm (SYN-DER) were evaluated using 124 Kompetitive allele specific PCR (KASP) functional assays on 87 functional genes. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn D3), thousand-grain weight (TGW) (TaCKX-D1, TaTGW6-A1, TaSus1-7B and TaCwi D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranging from 96.4-100%. The association analysis of functional genes with agronomic phenotypes in WW and WL conditions revealed that 21 marker-trait associations (MTAs) were consistently associated with agronomic traits in both conditions. Vrn-A1, Rht-D1, and xiv Ppd-B1 exhibited confounding effect on several agronomic traits including plant height, TGW and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced TGW in diversity panel. CWI gene has a conserved WECPDF domain. The result showed that 123 accessions have Hap 4A-C haplotype at TaCwi-A1, which is significantly associated with TGW and other agronomic traits under both WW and WL conditions. The non-synonymous substitutions observed in TaCwi-B1 in the conserved domain (WECPDF) were Glu372Lys, Glu372Gly, Pro374Gln, Asp375Thr, while Phe376Leu, Tyr377Thr, Val379Cys variants. In silico analysis revealed that these point mutations were sequentially and structurally influencing the biological function of the TaCwi-B1 protein.