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.