The mechanism of graft incompatibility is not yet fully understood and many reports focus on this problem in order to understand the mechanisms of graft development. Graft incompatibility is reported due to the Structural or Anatomical reasons, physiological and biochemical reasons, nutritional deficiency and presence of viruses at an early phase in response to grafting, as well as the consequences of these events on the future graft response. All these abnormalities result in mechanical weakening of the union, which may manifest the first year after grafting or may appear several years later, leading to major economic losses. Successful union of stock/scion involves lining up of vascular cambiums, subsequent wound healing response, callus bridge formation, wound repair xylem and phloem occur in the callus bridge just prior to initial cambium formation, the vascular cambium is completed across the callus bridge and is forming secondary xylem and phloem. The phloem mobile proteins have been reported that cross the graft interface when graft bridging is established and is functional. Commercial fruit trees are usually formed by the combination of a rootstock and a scion to broaden the adaptability of scion cultivars to soil and climatic conditions, facilitate agricultural management, and/or increase productivity. Graft incompatibility is a problem in cherry, almond, and apricot than in peach or plum, pear or quince. In general, closely related cultivars species unite readily and grow as a composite plant and that of unrelated plant do not. Even sometimes stock/scion of unrelated species unites initially and develops symptoms of incompatibility later and die eventually. An early and accurate prediction of graft incompatibility has great importance because incompatible combinations could be avoided while compatible ones could be selected. The complexity of incompatibility and the mechanism behind the reactions have been investigated in several ways. Moreover, research is needed to fully understand the mechanism of graft incompatibility, particularly in woody plants. This knowledge is essential to develop molecular markers useful in rootstock breeding programs.

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