Paclobutrazol Resistance (PRE) genes encode atypical basic helix–loop–helix (bHLH) transcription factor family. Typical bHLH proteins contain a bifunctional structure with a basic region involved in DNA binding and an adjacent helix–loop–helix domain involved in protein–protein interaction. PRE members lack the basic region but retain the HLH domain, which interacts with other typical bHLH proteins to suppress or enhance their DNA-binding activity. PRE proteins are involved in phytohormone responses, light signal transduction, and fruit pigment accumulation. However, apple (Malus domestica) PRE protein functions have not been studied. In this study, nine MdPRE genes were identified from the apple GDDH13 v1.1 reference genome and were mapped to seven chromosomes. The cis-acting element analysis revealed that MdPRE promoters possessed various elements related to hormones, light, and stress responses. Expression pattern analysis showed that MdPRE genes have different tissue expression profiles. Hormonal and abiotic stress treatments can induce the expression of several MdPRE genes. Moreover, we provide molecular and genetic evidence showing that MdPRE4.3 increases the apple’s sensitivity to NaCl, abscisic acid (ABA), and indoleacetic acid (IAA) and improves tolerance to brassinosteroids (BR); however, it does not affect the apple’s response to gibberellin (GA). Finally, the protein interaction network among the MdPRES proteins was predicted, which could help us elucidate the molecular and biological functions of atypical bHLH transcription factors in the apple.

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Plants mainly uptake inorganic nitrogen from soil as ammonium and nitrate. Less energy is required to assimilate ammonium compared to nitrates, and plants prefer to take up ammonium when the external nitrogen concentration is low. Investigating the patterns and mechanisms of ammonium absorption can help improve crop nitrogen utilization. In this study of apple, we isolated MdSAT1, a gene encoding an ammonium-responsive bHLH transcription factor. MdSAT1 promoted the growth and development of lateral roots and root hairs. Overexpression of MdSAT1 increased the transcript levels of genes related to ammonium uptake and assimilation and promoted the activities of ammonium assimilation-related enzymes, indicating that MdSAT1 can enhance ammonium uptake and utilization. MdSAT1 also can modulate ROS accumulation to ultimately regulate plant growth. Taken together, these findings provide insight into the mechanisms by which MdSAT1 controls ammoniun utilization as well as plant growth and development in apple.