| Summary: | The aim of this study was to prove that under <i>in vitro</i> conditions, the adhesiveness of the callus between rootstock and scion, the development of callus cells at the points of fusion, and the presence of phenolic components are closely related to the level of (in) compatibility of the grafting combinations between <i>Sato-zakura</i> cherry cultivars (‘Amanogawa’, ‘Kanzan’, and ‘Kiku-shidare-zakura’) and commercial rootstocks. <i>Prunus avium</i>, <i>Prunus</i> ‘Colt’, <i>Prunus mahaleb</i> and <i>Prunus serrulata</i> were used as compatible and <i>Prunus serotina</i> and <i>Pyrus communis</i> ‘Pyrodwarf’ were used as two potentially incompatible rootstocks. The results indicated the significant manifestations of the early signs of the incompatibility on the callus junction. Phenols, as well as tissue senescence, were very precisely localized by toluidine blue and alcian blue as well as safranin staining, which can indicate the early signs of the callus incompatibility in some grafting unions. In the callus unions of <i>Prunus avium</i> with ‘Amanogawa’ and ‘Kiku-shidare-zakura’ the results of chemical analyses indicated that the existence of several flavonols, flavones and phenol acids could be involved in the incompatibility process in grafted combination. The detection of flavonol astragalin in the unions can be a biomarker of compatibility between scion and the rootstock, while some polyphenols, such as neochlorogenic acid, sinapic acid, ellagic acid, caffeic acid, baicalein, naringenin, apigenin and luteolin can be used as the indicators of graft incompatibility. <i>p</i>-coumaric acid and ferulic acid could be used for detection of delayed incompatibility.
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