| Summary: | <i>Casuarina glauca</i> grows in coastal areas suffering long-term damage due to high salt stress. Arbuscular mycorrhizal fungi (AMF) can colonize their roots to alleviate the effects of salt stress. However, the specific molecular mechanism still needs to be further explored. Our physiological and biochemical analysis showed that <i>Rhizophagus irregularis</i> inoculation played an important role in promoting plant growth, regulating ion balance, and changing the activity of antioxidant enzymes. Transcriptome analysis of roots revealed that 1827 differentially expressed genes (DEGs) were affected by both <i>R. irregularis</i> inoculation and NaCl stress. The enrichment of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that most of these DEGs were significantly enriched in ion transport, antioxidant enzyme activity, carbohydrate metabolism, and cell wall. <i>HAK5</i>, <i>KAT3</i>, <i>SKOR</i>, <i>PIP1-2</i>, <i>PER64</i>, <i>CPER</i>, <i>GLP10</i>, <i>MYB46</i>, <i>NAC43</i>, <i>WRKY1</i>, and <i>WRKY19</i> were speculated to play the important roles in the salt tolerance of <i>C. glauca</i> induced by <i>R. irregularis</i>. Our research systematically revealed the effect of <i>R. irregularis</i> on the gene expression of <i>C. glauca</i> roots under salt stress, laying a theoretical foundation for the future use of AMF to enhance plant tolerance to salt stress.
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