The stress resistance and growth of the rootstock of grafted plants are influenced by scion traits, but the underlying mechanism is unclear in apple. Thus, we performed an RNA-seq analysis and examined the physiological and biochemical indices of seedlings generated by grafting wild-type (WT) or increased-branching mutant (MB) scions on Malus robusta rootstock. A functional analysis of RNA-seq data revealed plant–pathogen interaction was the most significantly enriched pathway among the differentially expressed genes in the axillary buds and roots of MB and WT samples. Most of the genes associated with plant–pathogen interactions, flavonoid biosynthesis, carotenoid biosynthesis, regulation of autophagy, natural killer cell-mediated cytotoxicity, the peroxisome, biosynthesis of unsaturated fatty acids, and the phagosome had up-regulated expression levels in the roots of MB grafted plants. The leaf water potential and the water loss rate were respectively lower and higher in MB leaves than in WT leaves. The chlorophyll content and photochemical efficiency were significantly lower in MB leaves than in WT leaves. Additionally, nitrogen, phosphorus, and potassium contents were significantly higher in the roots of the MB grafted seedlings than in the WT grafted seedlings. The glucose and fructose contents were unchanged in the MB roots, but not in the leaves and stems. The ABA, MDA, and H 2 O 2 levels were significantly higher in the MB grafted seedlings than in the WT grafted seedlings, whereas the opposite trend was observed for the antioxidant enzyme activities, especially in the roots and leaves, which was in accordance with the down-regulated expression of the genes related to antioxidant enzyme synthesis. These changes in the MB grafted seedlings were apparently due to MB scion characteristics, suggesting that rootstock vitality in grafted apple trees may be affected by the nutrient distribution, hormone status, and antioxidative stress tolerance of the scion
