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Malus hupehensis seedlings were treated with exogenous applications of IBA (0.1 mg L −1 and 0.5 mg L −1 ) in order to investigate the mechanism by which IBA promotes and effects lateral root (LR) development. Root morphology, plant height, plant crown diameter, and endogenous levels of hormone in LRs were evaluated. Additionally, patterns of differential gene expression related to root development were examined by RT-qPCR in IBA-treated and untreated roots during LR development. Results indicated that IBA treatment promoted both root and shoot growth, and that 0.5 mg L −1 IBA had a more obvious effect on growth promotion than 0.1 mg L −1 IBA. IBA treatment also induced an increase in the levels of endogenous auxin (IAA), zeatin-riboside (ZR), and the ratios of IAA/ABA and ABA/GA 1+3 , however, reduced gibberellin (GA 1+3 ) and abscisic acid (ABA) levels. In addition, there was also a significant upregulation in the expression of MdYUCCA4 , MdPIN1 , MdPIN2 and MdAUX1 in response to the IBA treatment; thus leading to an increase in auxin levels. Although MdIAA23 was induced, the expression of MdIAA5 and MdIAA14 , a negative regulator of MdARF7 and MdARF19 , were downregulated in IBA-treated apple seedlings. This resulted in elevated expression of MdARRO1 , MdGATA1 and MdSCR1, which was associated with an increase in lateral root development. Additionally, higher levels of endogenous auxin elevated the expression of MdWOX11 , and thus the expression of MdWOX5 , MdLBD16 and MdLBD29 ; collectively resulting in enhanced expression of the cell cycle related gene: MdCYCD3;1 . This pattern of expression was again associated with a promotion in lateral root development. In summary, changes in gene expression and hormone levels resulted in an increased number of LRs and other root growth parameters in IBA-treated plants. [ABSTRACT FROM AUTHOR]