This book was prepared to describe the scientific principles of the construction of genetic maps using an intera-specific F2 population and two PCR-based markers RAPDs and AFLPs. The book also describes the utilization of the construction of genetic maps in plant breeding programs, including gene(s)/QTL(s) mapping of desired traits, gene(s) isolation and gene(s) transfer. The mapped gene(s) can be used successfully in marker assisted selection (MAS) programs. This book will be a value added scientific resource for the MSc and PhD students who are interested to do their thesis s and dissertations in the field of plant genome, gen(s) and QTL(s) mapping. Simultaneously, the presented work well be a helpful lab manual for the young scientists and Post-Doc researchers due to the powerful information, protocols , techniques and detailed statistical methodology were included in the book chapters.