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. (c) 2007 Elsevier B.V. All rights reserved.