Abstract
Over the past two decades tremendous progress has been made in the area of genomics of crop plants, especially evolution of large number of high-throughput cost effective molecular markers and genotyping platforms which have helped to identify, map, and introgress alien genes from the wild backgrounds. The alien genes once mapped have been introgressed into cultivated crop plants through marker-assisted backcrossing (MABC) for improving biotic and abiotic stresses in major crop species including rice, wheat, chickpea, cotton, tomato, etc. Molecular markers associated with favorable alien QTL of wild species have an important role in introgression and tracing of these QTL during their transfer into the background of cultivated species. Thus these have become important for exploitation of alien genes in crop improvement. This chapter discusses the role of molecular markers in crop improvement through alien gene transfer.