InDel markers distinguish Basmatis from other fragrant rice varieties

Two alternative PCR-based marker systems were tested for polymorphism in a set of fragrant and non-fragrant rice (Oryza sativa L.) varieties. Markers based on InDels (sequences with an insertion/deletion) gave reliable polymorphisms that split Basmatis and other varieties into different groups, however, markers based on Rim2/Hipa transposons were less reliable or informative. Of 42 InDels tested, 71% showed polymorphisms between Basmati varieties and non-Basmati indicas. A sub-set of nine InDel markers was selected as a reliable test to distinguish between Basmatis and other fragrant rice varieties using high-resolution agarose gels. Both marker systems tested are suitable for rice breeding and genetic analysis in laboratories where polyacrylamide gels or sequencers are not available.