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Apple is an edible fruit of the apple tree Malus domestica L. and is widely grown worldwide. The genus Malus L. includes tremendous species that represent major vegetable crops having highly agronomic traits. This book reviews the utilization of biochemical and molecular markers for evaluating the genetic variation and phylogenetic relationships of Apple germplasm in order to provide developed strategies for crop improvement. This book is of interest to plant geneticists, plant breeders, researchers, and scientists.