The fragrant Indian Basmati rice and the Thai Jasmine rice are two of the most expensive and popular rice varieties in the world. A study published in the Proceedings of the National Academy of Science reports that the fragrance is due to the mutation of the gene called BADH2. The study reports eight novel mutations in the gene which are all associated with fragrance in Japonica (Basmati) and in Indica variety (Jasmine).

Further genetic analysis also revealed that the major fragrance allele originated in a Japonica-ancestor of Basmati rice which was later transferred to Indica varieties. The study authored by Susan McCouch and student Michael Kovach also confirmed two important findings: that Basmati rice is a true Japonica rice, and that the fragrance gene originated from Basmati and not from the Thai Jasmine rice. 

For details, see the article at http://www.news.cornell.edu/stories/Sept09/RiceFragrance.html