Narrow genetic diversity of Korean commercial rice lines have been a major limit factor in breeding new breeding lines having resistance and tolerance against biotic and abiotic stresses. Introducing novel favorable allele types could be possible through crossing with wild relatives, it demands additional tedious efforts to restore the unique genetic background of the recurrent parents, which determine commercial value in the market. Our study is preliminary based on the mutation breeding, by which agronomic traits could be acquired with the least impact on the unique haplotype of the wild type. Through screening and evaluating more than 7,000 mutant lines of Namil, a high yielding Korean japonica cultivar, several dozens of mutant lines expressing improved performances in terms of resistance or tolerance against biotic or abiotic stresses. One Sodium azide treated mutant line, Namil(SA)M2-1063-11-1-1-1-1-1-1, designated as ‘Namil(SA)-bl5’ performed high level of resistance against rice blast as well as reduced culm length. Two mapping populations, to dissect genetic basis of the blast resistance and short culm length, were constructed by using F2 progenies derives crosses between Namil(SA)-bl5 and Milyang23 and Namil(wild type) and Milyang23. Each progenies were evaluated in terms of DNA marker genotype as well as basal agronomic traits including blast resistance by using F2:3 seeds. Association analysis between marker genotype and evaluated phenotype of progeny lines were adopted to localize the putative chromosomal locations involved to culm length and blast resistance. The putative locations unique to Namil(SA)-bl5 were then elucidated through the comparisons with those of Namil x Milyang23 reference population. Tentatively, the genetic factors for reduced culm length and blast resistance were identified on chromosome 7 and chromosome 12, respectively.