Root-associated endophytic fungi like Serendipita indica and arbuscular mycorrhizal(AM) fungi can improve plant growth and root construction, but the potential mechanism is unclear. In this study, Funneliformis mosseae(an AM fungus) and S. indica, singly or in combination were inoculated into trifoliate orange(Poncirus trifoliata) seedlings, to assess changes in biomass and root morphological traits, coupled with auxins and cytokinins concentrations in leaves and roots and the expression of auxin synthesis and transporter protein genes. After 20 weeks of inoculation with these fungi, shoot and root biomass, root total length, taproot length, average diameter, surface area, volume, and the number of lateral roots in 1st-, 2nd-, and 3rd-order were improved, and S. indica showed a relatively greater effect than F. mosseae and dual inoculation. Endophytic fungal inoculation also significantly increased the concentration of indoleacetic acid, indole butyric acid, trans-zeatin,dihydrozeatin, and isopentenyl adenine in leaves and roots, whilst F. mosseae and S. indica exhibited relatively greater effects on leaves and roots, respectively. Correlation analysis revealed that both biomass and root morphological traits(except root projected area) were significantly positively associated with endogenous auxins and cytokinins. In addition, the inoculated plants recorded comparatively higher expression levels of indoleacetic acid synthesis genes(PtTAA1, PtTAR2, PtYUC3, PtYUC4, PtYUC6, and PtYUC8) and indoleacetic acid transporter protein genes(PtAUX1, PtLAX1, PtLAX2, PtLAX3, PtPIN1, PtPIN3, PtPIN4, PtABCB1, and PtABCB19) than the non-inoculated plants, among which F. mosseae and S. indica showed better effects in leaves and roots, respectively. These results suggest that root-associated endophytic fungi improved plant growth and root architecture, which were associated with changes in endogenous auxins and cytokinins.
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