Wheat\u2014a staple food crop of many countries, has always been a target for improving its resilience to biotic and abiotic stresses. Among these, rust diseases are the most detrimental in depressing wheat production. In the present study, chemical mutagen was used to induce mutations in a wheat variety NN-Gandum-1 (moderately resistant to leaf and yellow rust) for improving resistance to the disease as well as studying function of genes conferring resistance to the disease. In the present investigation, 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91 %) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Maximum number of mutations were found in introns. Highest number of SNPs were detected in chr.2B (14,273 SNPs). Mutation density was one mutation per 20.91 Mb. Highest mutation frequency was found in chr.7D (1\/2.83 Mb) and the lowest in chr.2D (1\/85.17 Mb). Out of the detected mutations, 101 SNPs were selected using priority analysis criteria. Out of these, SNPs detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in NBS domain of chr.1BS at 3.4 Mb that possibly activated the function of chimeric allele. Through computational analysis, it was demonstrated that identified SNP substituted the glutamic acid with alanine\u2014resulted in altered protein structure. It was concluded that induced mutations are extremely helpful not only in generating novel genetic resource but can also exploited for getting insight into the important biological circuits of different traits of complex genomes like wheat.