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Background  The close planting of dwarfing self-rooted rootstocks is currently a widely used method for apple production; however, self-rooted rootstocks are weak with shallow roots and poor grounding. Therefore, understanding the molecular mechanisms that establish the gravitropic set-point angles (GSAs) of the adventitious roots of self-rooted apple stocks is important for developing self-rooted apple rootstock cultivars with deep roots.    Results  We report that the apple FOUR LIPS (MdFLP), an R2R3-MYB transcription factor (TF), functions in establishing the GSA of the adventitious roots of self-rooted apple stocks in response to gravity. Biochemical analyses demonstrate that MdFLP directly binds to the promoters of two auxin efflux carriers,  MdPIN3  and  MdPIN10 , that are involved in auxin transport, activates their transcriptional expression, and thereby promotes the development of adventitious roots in self-rooted apple stocks. Additionally, the apple auxin response factor MdARF19 influences the expression of those auxin efflux carriers and the establishment of the GSA of adventitious roots of apple in response to gravity by directly activating the expression of  MdFLP .    Conclusion  Our findings provide new insights into the transcriptional regulation of  MdFLP  by the auxin response factor MdARF19 in the regulation of the GSA of adventitious roots of self-rooted apple stocks in response to gravity.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1847-2) contains supplementary material, which is available to authorized users.

Transcriptional regulation of MdPIN3 and MdPIN10 by MdFLP during apple self-rooted stock adventitious root gravitropism