Identification of Badh2 Mutation Type among Indonesian Fragrant Rice Varieties

Abstract

The premium price as well as the high and increasing world market demand for fragrant rice has triggered the development of various fragrance markers. The application of these markers on genotyping of various popular Indonesia rice varieties is reported in this paper.  PCR profiles of popular Indonesia non-fragrant (Ciherang, Fatmawati) and fragrant (Pandan wangi, Rojo Lele, Mentik Wangi, Gunung Perak, Pulu mandoti, Pare Kembang, Sintanur) rice varieties were compared using aromatic markers of  Bradbury et al. (2005b), Lang and Buu (2008), Shi et al. (2008), and Sakthivel et al. (2009). For comparison, IR64, Nipponbare and Taipei 309 varieties were included. Rice genomic DNA was isolated from young leaves using the method as described by Doyle and Doyle (1990), PCR amplified using each of the above fragrance markers and PCR products were analysed by agarose-gel-electrophoresis. Fragrance markers of Bradbury et al. (2005b), Shi et al. (2008), and Sakthivel et al. (2009) were only able to discriminate fragrant Mentik Wangi and Gunung Perak from non-frangrant rice varieties, while other fragrant rice varieties (Pandan wangi, Rojo Lele, Pulu mandoti, Pare Kembang, Sintanur) showed similar band patterns as those of non-frangrant rice varieties. This suggests there are at least two groups of badh2-deletion patterns among Indonesia fragrant rice varieties. Group 1 include Mentik Wangi and Gunung perak, while group 2 includes Pandan wangi, Rojo Lele, Pulu mandoti, Pare Kembang and Sintanur.  Only the RM 223 marker of Lang and Buu (2008) was able to distinguish both fragrant groups from non-fragrant Ciherang. The difference in RM233-amplicon sizes between fragrant groups 1 and 2, also supports the variation of badh2 mutation pattern among Indonesia fragrant rice.

Keywords: Bradbury, Badex7-5, FM-E7, FM-E2A, RM 223, fragrance, Pandan Wangi