Houba retrotransposon-based molecular markers: a tool for variation analysis in rice

Abstract

Rice is one of the most important crop plants as well as a model organism used for genetic studies. Transposons, especially retrotransposons, have a significant impact on the rice genome. A considerable percentage of the rice genome is composed of transposons (about 35%). Thus, transposons are an important internal factor for the genome evolution of rice varieties. In this study, we performed fingerprint analyses of 37 Oryza sativa L. cultivars using an IRAP marker. For this purpose, we designed IRAP primers specific to Houba (Tos5/Osr13), RIRE1 and Hopi (Osr27), and Osr30 retrotransposons, the most abundant retrotransposons in the rice genome. Polymorphism ratios were calculated with Jaccard similarity index. Our results showed that 37 cultivars of rice have a variable range of polymorphisms. The maximum polymorphisms were 75% for Hopi, 57% for Osr30, 52% for Houba, and 45% for RIRE1. Although these are high percentages of polymorphisms, all cultivars had a certain number of identical bands in all tested retrotransposons. These results prove that retrotransposon-based marker techniques could be useful for identification of cultivars in rice. Houba in particular is a good candidate for rice fingerprinting because of its band pattern quality.