Over the past two-three decades, several genetic/DNA marker systems have been developed and put into use in both animal and plant systems for a variety of genetic analyses. Since then, the use of different DNA marker systems in genetic analysis and manipulation of complex traits in plant breeding has exponentially progressed. DNA markers have great potential to enhance effi ciency of plant breeding and have shown signifi cant promise in several applications like fi ngerprinting and identifi cation of genetic stocks, genetic diversity assessment, seed purity, phylogenetic analysis, early generation selection, backcross breeding, etc. Nevertheless, their greatest potential lies in their use for accelerating the genetic gain in plant breeding and in identifying Quantitative Trait Loci (QTL) or genes involved in trait expression especially for those with economic importance. For the effective genetic manipulation of complex traits, the map positions of genes and the linked markers on a chromosome need to be determined. It is, therefore, essential to develop DNA marker based genetic maps in a crop species.