The root architecture of grafted apple (Malus spp.) is affected by various characteristics of the scions. To provide information on the molecular mechanisms underlying this influence, we examined root transcriptomes of M. robusta rootstock grafted with scions of wild-type (WT) apple (M. spectabilis) and a more-branching (MB) mutant at the branching stage. The growth rate of rootstock grafted MB was repressed significantly, especially the primary root length and diameter, and root weight. Biological function categories of differentially expressed genes were significantly enriched in processes associated with hormone signal transduction and intracellular activity, with processes related to the cell cycle especially down-regulated. Roots of rootstock grafted with MB scions displayed elevated auxin and cytokinin contents and reduced expression of MrPIN1, MrARF, MrAHP, most MrCRE1 genes, and cell growth-related genes MrGH3, MrSAUR and MrTCH4. Although auxin accumulation and transcription of MrPIN3, MrALF1 and MrALF4 tended to induce lateral root formation in MB-grafted rootstock, the number of lateral roots was not significantly changed. Sucrose, fructose and glucose contents were not decreased in MB-grafted roots compared with those bearing WT scions, but glycolysis and tricarboxylic acid cycle metabolic activities were repressed. Root resistance and nitrogen metabolism were reduced in MB-grafted roots as well. Our findings suggest that root growth and development of rootstock are mainly influenced by sugar metabolism and auxin and cytokinin signaling pathways. This study provides a basis that the characteristics of scions are related to root growth and development, resistance and activity of rootstocks.

Flavonoids are a class of polyphenol compounds that are widespread in plants. They play an important role in plant growth and development. In this study, we found a mutant strain of M. baccata with yellow leaves (YL). Transcriptome sequencing revealed that it exhibited significant changes in the flavonoid metabolism pathway, which screening revealed was associated with a glycosyltransferase gene, MD09G1064900 (MdGT1). Analysis of its spatiotemporal expression showed that MdGT1 was mainly expressed in the stem and leaves, it means that MdGT1 may have a functional role in these parts. Real-time PCR and HPLC showed that MdGT1 was significantly upregulated by anthocyanin and exhibited strong anthocyaninase activity in vitro, respectively. An MdGT1 plant expression vector was constructed and overexpressed in apple fruit callus, resulting in a significant decrease of anthocyanin. Phenotypic observation also revealed that the MdGT1-overexpressing lines exhibited worse growth than the wild type after NaCl treatment, while they grew better upon the addition of exogenous anthocyanins. Moreover, real-time PCR and physiological data showed that MdGT1 is involved in salt stress and closely related to antioxidant pathways. Electrophoretic mobility shift assays (EMSA) and yeast one-hybrid experiments also proved that the transcription factor MdMYB88 is an upstream regulatory factor of MdGT1. The sequencing results revealed an amino acid insertion in an MdMYB88 HTH domain (between 77-131 amino acids) in the YL mutant strain. In conclusion, we identified a new apple glycosyltransferase gene, MdGT1, which may affect the color of apple leaves by glycosylating anthocyanins, and be regulated by the upstream transcription factor MdMYB88. Significance statement The glycosyltransferases and their physiological significance in apple are largely unknown. Here we revealed that the MdMYB88-regulated apple glycosyltransferase gene MdGT1 plays a crucial role in the color of apple leaves and enhances plant tolerance to salt by antioxidant pathways via anthocyanin metabolism.