Retrotransposon-based molecular markers ; Tools for variation analysis in plants

Molecular marker is a nucleotide sequence associated with a trait of interest. Molecular marker techniques are based on either hybridization or Polymerase Chain Reaction (PCR) and rely on DNA polymorphisms between samples. Various PCR-based markers are widely used for diverse purposes and their technical properties have been widely explored. New and improved techniques have been developed by a combination of different strategies e.g. cDNAs, enzyme digestion or the utilization of specific sequences e.g. expressed sequence tags (ESTs), microsatellites, retrotransposons. Retrotransposons are a class (Class I) of transposable elements (TE) and constitute a major portion of the genome in plants with large genomes. They are important for chromatin modifications and epigenetic reprogramming. Retrotransposons are also an ideal target for developing molecular marker techniques because of their amplification mechanism and sequence characteristics. There are different types of transposon based marker techniques. Some of them are; Inter-Retrotransposon Amplified Polymorphism (IRAP), Retrotransposon-Microsatellite Amplified Polymorphism (REMAP), inter Primer Binding Site Correspondence/Reprint request: Dr. Nermin Gozukirmizi, Istanbul University, Faculty of Science, Department of Molecular Biology and Genetics, 34134, Vezneciler-İstanbul, Turkey. E-mail: nermin@istanbul.edu.tr Nermin Gozukirmizi et al. 20 amplification (iPBS), Sequence-Specific Amplification Polymorphism (S-SAP), Retrotransposon Based Insertion Polymorphism (RBIP), Inter Sine Amplified Polymorphism (ISAP), RAPD-Retrotransposon Amplified Polymorphism (RRAP), Inverse Sequence Tagged Repeats (ISTR), Inter-MITE Polymorphism (IMP) and Transposable display (TD). These methods are the most widely used for different breeding strategies like; the determination of candidate genes, genetic variability, linkage, genome mapping, the DNA fingerprinting, phylogenetics, systematics, conservation, molecular ecology, somaclonal variation studies, transgenic research, developmental biology, and mutagenesis. In this review article after a brief introduction and review of different types of retrotransposon-based markers, we discuss their potential applications in plant biology and also present our recent research data on sources of somaclonal variation in barley.