This edited book covers the applications of molecular markers in the genetic improvement of crop plants. Recent advances in molecular marker techniques such as the development of high-throughput genotyping platforms, marker-assisted selection, and non-coding RNA-based markers have been discussed. Essential information is provided on functional markers, genotype-by-sequencing, and association mapping methodologies that can facilitate accelerated crop breeding programs for increased yield, high nutritional quality, and tolerance to a variety of abiotic and biotic stresses. This volume presents basic information on molecular marker techniques from marker location up to gene cloning. The book includes a description of technical approaches in genome analysis such as comparison of marker systems, positional cloning, and array techniques. This book is of interest to teachers, researchers, and plant breeders. The book also serves as additional reading material for undergraduate and graduate students of agriculture, horticulture, and forestry.