Soybean [Glycine max (L.) Merr.] seeds are abundant in high-quality proteins and fats. In addition, soybean seeds are also rich in secondary metabolites, such as isoflavones, lecithin, and saponins. Triterpene saponins are major components of these physiologically active metabolites in soybean seeds. Soybean saponins are classified as group A and DDMP saponins. Among them group A saponins are undesirable component of food products due to bitterness and astringency and also cause foaming in tofu production. Whereas, DDMP saponins and their derivatives are less bitter and astringent and beneficial to human health when consumed as regular diet. Therefore, reducing the group A saponins or increasing the DDMP saponins are required to improve the food quality. The present study focused to identify and characterize the gene which is encoding a protein responsible for biosynthesis of DDMP saponins. EMS mutant lines (sg-7-1 & sg-7-2) which lack DDMP saponins were developed. The breeding cross has been made with these two mutants with two cultivars, Pungsannamul and Wooram to study the segregation and genetic linkage analysis, respectively. The segregation analysis showed that the mutant phenotype is controlled by single recessive gene. TLC analysis for phenotyping F2 population of Wooram X sg-7-1 showed mutant, wild and heterozygous types. To surprise two more patterns were detected and they were named as strange type1 (ST1) and strange type2 (ST2). Further, SSR marker analysis will be carried out to locate the gene which encoding a protein responsible for biosynthesis of DDMP saponins.