Chakravarthy Rajan's research focuses on genetic engineering of rice and pearl millet for crop improvement, which includes molecular cloning, tissue culture, and transformation studies.

Most of the commercially important chemicals made by plants are produced as part of their secondary metabolism. The majority of secondary metabolites are generally produced in low quantities in their host plants and their isolation suffers from low yield and high consumption of natural resources, which are driving some plants and forests to near extinction. Aromatic Mint plants of Mentha species are easy to cultivate and harvest and they are the source of the best known monoterpene chemical, Menthol, which is the principal component of peppermint essential oil. In his previous Lab at TTL, Rajan established a transformation system and hairy root culture in Mint and Sweet Basil.