Aims One of the major limitations to the production of alfalfa (Medicago sativa) is the fungus Phoma medicaginis, which infects alfalfa and causes leaf spots. This study aims to understand alfalfa’s response to P. medicaginis infection, the colonization of arbuscular mycorrhizal fungus (AMF) and the effect of AMF on plant–pathogen interactions. Methods and Results Transcriptome analysis (RNA-seq) was used to identify differentially expressed genes (DEGs) in alfalfa infected by P. medicaginis and colonized by AMF Rhizophagus intraradices. AMF ameliorated the effects of P. medicaginis infection on alfalfa by reducing leaf spot incidence and disease index by 39·48 and 56·18% respectively. Inoculation with pathogen and AMF induced the activity of defence pathways, including peroxidase (POD), polyphenol oxidase activities and jasmonic acid (JA), salicylic acid concentration. Plants showed differential expression of P. medicaginis resistance-related genes, including genes belonging to pathogenesis-related (PR) proteins, chitinase activity, flavonoid biosynthesis, phenylpropanoid biosynthesis, glutathione metabolism, phenylalanine metabolism and photosynthesis. Inoculation with AMF led to changes in the expression of genes involved in PR proteins, chitinase activity, phenylalanine metabolism and photosynthesis. Conclusion The physiological and transcriptional changes caused by P. medicaginis infection in non-mycorrhizal and mycorrhizal alfalfa provides crucial information for understanding AMF’s association with pathogenic systems. Significance and Impact of the Study This study showed that AMF alleviated alfalfa leaf spots demonstrating that AMF can serve as a biocontrol strategy for alfalfa disease management.

Perennial ryegrass (Lolium perenne) is widely cultivated around the world for turf and forage. However, the plant is highly susceptible to disease and is sensitive to drought. The present study aims to determine the effect of the fungal endophyte Epichloë festucae var. lolii of perennial ryegrass on the combined stresses of drought and disease caused by Bipolaris sorokiniana in the greenhouse. In the experiment, plants infected (E+) or not infected (E−) with the fungal endophyte were inoculated with Bipolaris sorokiniana and put under different soil water regimes (30%, 50%, and 70%). The control treatment consisted of E+ and E− plants not inoculated with B. sorokiniana. Plant growth, phosphorus (P) uptake, photosynthetic parameters, and other physiological indices were evaluated two weeks after pathogen infection. The fungal endophyte in E+ plants increased P uptake, plant growth, and photosynthetic parameters but decreased the malondialdehyde concentration, proline content, and disease incidence of perennial ryegrass (p < 0.05). E+ plants had the lowest disease incidence at 70% soil water (p < 0.05). The study demonstrates that the fungal endophyte E. festucae var. lolii is beneficial for plant growth and stress tolerance in perennial ryegrass exposed to the combined stresses of drought and B. sorokiniana.