The Use of Mobile Genetic Elements as Molecular Marker in Agricultural Biotechnology

The basis of molecular marker techniques are based on hybridization or Polymerase Chain Reaction (PCR). New and improved techniques have been developed as a combination of different strategies such as; cDNAs, enzyme digestion or the utilization of specific sequences; e.g. expressed sequence tags, microsatellites, and retrotransposons. Retrotransposons are a class (Class I) of transposable elements. Transposon elements physically form an important part of the genome in plants. Retrotransposons are also an ideal target for developing molecular marker techniques because of their amplification mechanism and sequence characteristics. Some of these are; Inter-Retrotransposon Amplified Polymorphism, Retrotransposon-Microsatellite Amplified Polymorphism, Inter Primer Binding Site Amplification, Sequence-Specific Amplification Polymorphism, Retrotransposon Based Insertion Polymorphism, Inter Sine Amplified Polymorphism, RAPDRetrotransposon Amplified Polymorphism, Inverse Sequence Tagged Repeats, Inter-MITE Polymorphism and Transposable display. These methods are used widely for different breeding purposes. Some of those are used in determination of genetic diversity, genetic linkage, genome mapping, DNA fingerprint analysis, phylogenetics, somaclonal variation studies, transgenic research, developmental biology, and mutagenesis studies. In this article, the common uses and potential applications of different retrotransposon-based marker types in agricultural biotechnology will be discussed