Fragrance character in rice is now known to affect the plant performance at larger extent. This rare metabolic disease caused due to synthesis of 2AP in rice is very complex to interpret. For better understanding, the differentially expressed genes due to mutation in BADH2 should be studied. Transformation of fragrant rice with functional BADH2 or silencing of BADH2 in non-fragrant rice can be done and differentially expressed genes can be studied. The in-silico analysis of these differentially expressed genes will help in better understanding the effect of 2AP biosynthesis on yield and low tolerance to stress in rice. As reported by several researchers, Δ1-pyrroline pool is considered important for synthesis of 2AP and GABA. The over expression of ornithine decarboxylase (ODC) and diamine oxidase (DAO) genes in rice will help in increasing Δ1-pyrroline pool and thus development of super rice variety with elevated 2AP concentration and yet with higher yield and tolerance to stress.