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Background  Melatonin (MT) is important for plant growth and development; however, it is not known whether MT is involved in apple adventitious root (AR) development. In this study, we treated  Malus prunifolia  (MP) at four different stages of AR development, and analyzed the level of the endogenous hormones MT, auxin (IAA), zeatin-riboside (ZR), abscisic acid (ABA), and gibberellins (GA 1 + 3 ) in all four treatment groups and the untreated control group. The expression of MT, IAA biosynthesis, transport and signal transduction, the cell cycle, and root development related genes were quantified by RT-qPCR. The function of  MdWOX11  was analyzed in transgenic apple plants.    Results  The promotion of AR development by MT was dependent on the stage of AR induction between 0 and 2 d in apple rootstocks. MT-treatment increased the level of IAA and crosstalk existed between MT and IAA during AR formation. The expression of  MdWOX11  was induced by MT treatment and positively regulated AR formation in apple. Furthermore, transgenic lines that overexpressed  MdWOX11  lines produced more ARs than ‘GL3’. Phenotypic analysis indicated that  MdWOX11  overexpression lines were more sensitive to exogenous MT treatment than ‘GL3’, suggesting that  MdWOX11  regulates AR formation in response to MT in apple rootstock .Conclusions  MT promotes AR formation mainly during the AR induction stage by inducing IAA levels and upregulating  MdWOX11 .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02747-z.

Melatonin promotes adventitious root formation in apple by promoting the function of MdWOX11