As a result of the continuous global warming in recent years, the average annual number of rain days in China has been on the decline, while the number of rainstorm days has gradually increased. These conditions make it extremely easy to form a waterlogging environment, which has an adverse impact on plant growth and development. In many apple-producing areas in China, apples are subject to severe flooding during planting. In this study, two-year-old apple rootstock M9T337 was used to explore the effects of interval water stress on the morphological and physiological parameters of apple leaves. The purpose was to determine the plant’s adaptability to waterlogged environments and provide theoretical reference for management and maintenance after waterlogging. The results showed that the effect on flooded (T2) on apple stock was greater than that of waterlogged (T1), Short-term (7 d) waterlogging (T1) did not affect the growth of seedlings but was conducive to the accumulation of dry matter. Furthermore, the initial stress was be imprinted on the plants, which could directly affect their response to later stress. The results of principal component analysis (PCA) revealed that PC1, PC2, and PC3 explained 26.92%, 17.46%, and 13.03% of the physiological changes under water stress, respectively. By calculating the weight of each indicator, we concluded that high-frequency resistance r, relative chlorophyll content (SPAD) and maximum photochemical efficiency Fv/Fm are important parameters for apple rootstocks affected by water stress.
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