Plant breeding, like several other classical fields of R&D in plant sciences has also been substantially influenced by the development and use of molecular markers. These markers have been found to be powerful tools for wide ranging applications in many plant breeding areas, notably, identification and analysis of quantitative/qualitative trait loci (QTLs) and their positioning on linkage maps; cloning of genes for desirable traits based on the molecular linkage maps; gene pyramiding and Marker-assisted selection (MAS), the determination and analysis of genetic diversity within germplasms and other plant collections and analysis of genome structures for several crop plants [1-4]. As applied in breeding programs, the molecular markers help to accelerate the incorporation of genes that control or contribute to the variation of the target traits and also provide reliable information of kinship and phylogeny between species. Considerable progress and achievements in the area of molecular marker research have been reported for more than three decades now, ever since the first molecular marker application as a RFLP was reported by Botstein et al. . Increasing applications of molecular markers and progressive improvements to the various technologies involved have also ensured that the molecular markers continue to be deployed for plant breeding work regularly [1-3,6-8]. Since the proposition of the concept in 1980, various types of molecular markers such as RFLP, RAPD, AFLP, SSR, SNP among others have been developed [5,9-15]. These markers vary in their resolution power, genome coverage and linkage or otherwise to loci controlling traits of relevance to the breeder. Likewise, these markers have also varying levels of complexities of experimental designs, ease of field level application and the need for advanced skill sets and resources for successful application in breeding strategies. Successful applications of these markers have depended on their deployment as markers of choice based on exhaustive studies over a large time period (more than 3 decades) and across a large number of crop plants. These markers have been developed as general markers while at the same time we also now have specific sets of molecular for specific crops that can be deployed with ease and high efficiency anywhere in the world.