Integrated transcriptomic and metabolomic analyses reveal the effect of mycorrhizal colonization on trifoliate orange root hair

•AMF promoted root hair growth in trifoliate orange.•Metabolisms of hormone, amino acid, penylpropanoids, fat and carbohydrate mediated citrus root hair growth under AMF.•Pectinesterase, ROP1, YUCCA2, Amidase, ABCB10, IAA17, PIN1b, GH3, ARF1 may be participated in the citrus root hair growth under AMF. Trifoliate orange (Pocirus trifoliata) as an excellent stock for citrus, but it has few root hairs and relies on mycorrhiza (AM) formed by arbuscular mycorrhizal fungi (AMF) to absorb soil nutrients and water, and there are few studies on the relationship between trifoliate orange root hair and AMF. This experiment analyzed the conditioning of AMF in trifoliate orange root hair growth from multiple perspectives. The results showed that AMF inoculation promoted root hair in citrus (eg: density and length) and the AMF mycorrhizal infection rate was 49.12 %. Metabolic and transcriptomic data of root also show that AMF promotes the development of root hair mainly by influencing hormone transduction and biosynthesis. The analysis of hormone synthesis signal transduction expression profile showed that AMF infection significantly up-regulated auxin, gibberellin, ethylene and cytokinin synthesis and signal transduction pathway, and also up-regulated auxin transport and jasmonic acid transduction. Analysis of root hair growth-related genes showed that AMF infection the up-regulated genes correlate with cell wall loosening, Ca2+ gradient and cell cycle, thereby facilitate the formation and elongation of root hair. In summary, AMF regulates trifoliate orange root hair growth through plant hormone metabolism and related key genes, thus increases the root surface area and further promotes the infection of AMF. In order to provide theory foundation for exploring the mechanism of AMF regulating trifoliate orange root hair growth.