Temperate climate fruit species are important fruit groups both in the world and in Turkey. Most of these fruit species because cannot be propagated by seeds due to the long generation period are propagated by grafting. Rootstocks affect many factors in cultivars such as growth vigor, yield and quality, and maturation time. Thanks to the rootstocks selected in grafting, resistance to soil-borne diseases and pests and resistance to abiotic stress conditions can be achieved. Ideal rootstocks should show compatibility very well with the varieties they are grafted on. Graft incompatibility is a major problem in rootstock breeding studies. The reasons for graft incompatibility have not been fully explained. Although anatomical studies on graft incompatibility give important opinions, there are many studies proving that biochemical analyzes also provide important results.