Molecular markers are heritable differences in nucleotide sequences of DNA at the corresponding position on homologous chromosome of two different individuals, which follow a simple Mendelian pattern of inheritance. Over the last two decades, the advent of molecular markers has revolutionized the entire scenario of biological sciences. DNA-based molecular markers are a versatile tool in the fields of taxonomy, physiology, embryology, genetic engineering, etc. (Schlotterer 2004). They are no longer looked upon in simple DNA fingerprinting markers in variability studies or in mere forensic tools. Ever since the development of molecular markers, these are constantly being modified to enhance the utility and to bring about automation in the process of genome analysis. The discovery of PCR (polymerase chain reaction) was a landmark in this effort and proved to be a unique process that brought about a new class of DNA profiling markers. This facilitated the development of marker based gene tags, genetic mapping, map-based cloning of agronomically important genes, genetic diversity studies, phylogenetic analysis, and marker-assisted selection of desirable genotypes etc. (Joshi et al. 2000).