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Nitrogen (N) is the main nutrient element limiting plant growth and crop yield. Plant proline-rich proteins (PRPs) are a group of structural proteins that are rich in proline and hydroxyproline. Previously, we identified 9 PRPs from the apple genome and found that they were induced by different stress treatments. In this study, we showed that the expression of MdPRP6 was inhibited by low N stress. Transgenic apple plants with decreased MdPRP6 expression were generated by RNA interference (Ri) to explore the biological role of MdPRP6 under low N stress. Ri transgenic apple plants grew better than wild-type (WT) plants under low N stress, as indicated by their well-developed roots; greater height, stem diameter, number of leaves, and biomass; and higher photosynthetic capacity and N content. N and starch metabolism were more active in Ri plants than in WT plants. Ri plants accumulated greater amounts of starch and soluble sugar under low N stress, which was consistent with the higher expression levels of related genes in Ri plants relative to WT plants. The accumulation of anthocyanins was higher in Ri plants than in WT plants under low N stress, which helped plants resist the effects of low N stress. The indole acetic acid (IAA) content was higher in the roots of Ri plants, which strengthened the root system. Overall, our data suggested that MdPRP6 negatively regulates low N stress tolerance by modulating anthocyanin accumulation and IAA metabolism in the roots of apple plants. • RNAi of MdPRP6 resulted in more LR in transgenic apples under LN stress. • RNAi of MdPRP6 conferred more accumulation of anthocyanins in transgenic apples under LN stress. • The tolerance of LN stress conferred by MdPRP6 was related to the soluble sugars content. [ABSTRACT FROM AUTHOR]