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Genome-wide association studies (GWAS) were undertaken to detect SNP markers related with physiological and biochemical traits in 92 genotypes from Pakistani historical set and synthetic hexaploid wheat collections. The field experiment was conducted during 2013-2015 seasons under controlled and drought conditions. Genotyping was done using high-density Illumina iSelect 15K SNP (single nucleotide polymorphism) array, and finally 7739 high quality SNPs were used in mapping. Linkage disequilibrium decay was observed at 11cM genetic distance for whole genome collection using 700 unlinked markers. In total, there were 1174 MT As recorded for biochemical parameters at P<O. 001 in stressed conditions using MLM approach, among them, 647 MTAs were flanked for more then one trait. Genome A, B and D contributed 431, 553 and 190 MTAs respectively. Highest number of MTAs were found on chromosome 2B. Further FDR test was used to detect noval MTAs discussed in paper