To better understand the genetic relationships between quantitative and qualitative characteristics of rice, the most important agronomic traits, seed physicochemical properties, and storage protein compositions were evaluated in different quantitative and qualitative cultivars including two new mutant cultivars, their parents and their common ancestor. The result of agronomic traits shows that two mutant cultivars, Roshan and Shahryar, have the highest yield (8500 and 8000 kg/ha respectively) accompanied by some desirable agronomic characteristics such as lodging resistance, early maturity period, a high number of tillers and high panicle length. The qualitative properties evaluation also revealed these two novel mutant cultivars were characterized by good cooking and eating properties. Roshan has moderate amylose content (AC), and both were similar to Sangetarom, a qualitative cultivar, in terms of gelatinization temperature (GT) and gel consistency (GC). The recessive variant of the BADH2 gene was also observed in Roshan and Sangetarom. Moreover, the Shahryar cultivar showed a significant decrease in prolamin protein when compared to the parent and the other cultivars. Generally, no significant relationship was detected between agronomic characteristics and yield with seed biochemical properties, such as cooking and eating quality, fragrance and storage protein content. These results promise that by identifying and pyramiding desirable alleles, especially alleles involved in starch synthesis, fragrance and prolamin protein biosynthesis, can lead to obtaining rice cultivars with higher quantitative and qualitative properties.