Apple cultivars are one of the main factors setting the composition of bioactive compounds in apples and the quality of the fruit. However, research has been providing increasing amounts of data on the influence of rootstocks on the variations in the composition of bioactive compounds in apples. The aim of the study was to determine the influence of rootstocks on the changes in the qualitative and quantitative composition of phenolic compounds and their antioxidant activity in vitro in apple flesh and peel. HPLC analyses of phenolic compounds in apple samples were performed. The rootstock–scion combination had a significant effect on the composition and antioxidant activity of phenolic compounds in apple samples. Depending on the rootstock, the total content of phenolic compounds in apple flesh of the ‘Galaval’ cultivar could vary by 2.9 times, and in the peel by up to 90%. The genotype of the rootstock resulted in the highest variation in total flavan-3-ol content in apple flesh—by as much as 4.3 times—while the total content of flavonols varied by 2.1 times. In apple peel, on the contrary, the greatest variation was recorded for the total flavonol content (by 4.4 times), and the total flavan-3-ol content varied the least (by 1.8 times). A proper match of a cultivar and a rootstock can program a fruit tree to grow larger amounts of higher-quality, antioxidant-rich, and high-nutrition-value fruit.

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