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Background   Pinus massoniana  Lamb. is an important afforestation tree species with high economic, ecological and medicinal values. Aluminum (Al) toxicity driven by soil acidification causes dieback of  P. massoniana  plantations. Previous studies showed that ectomycorrhizal fungi alleviate Al stress damages in  Pinus , but the underlying molecular mechanisms and key genes induced by ectomycorrhizal fungi inoculation under Al stress in  Pinus  have not been explored. Herein, we applied Al stress for 60 days to  P. massoniana  seedlings inoculated with  Suillus luteus  (SL) and those non-inoculated. Then, we compared their growth parameters and transcriptome in order to detect candidate genes induced by SL conferring Al tolerance in  P. massoniana .    Result  Our results showed that SL inoculation confers Al stress tolerance in  P. massoniana  through improved growth performance, strong antioxidant enzyme activities and reduced malondialdehyde accumulation as compared to non-inoculated seedlings. Transcriptome sequencing further supported these findings as very few genes (51 genes) were transcriptionally altered by Al in SL inoculated plants as compared to non-inoculated plants (2140 genes). We identified three core genes ( cox1 ,  cox3  and  Nd1 ) that were strongly up-regulated by Al in the SL inoculated plants but were down-regulated in the non-inoculated plants. We also identified 42 genes specifically regulated by SL inoculated plants under Al stress, which are involved in a wide range of biological processes such as antioxidative response, transporters, hormone signaling and plant pathogen infection responses.    Conclusions  Altogether, our data suggest that SL inoculation induces priming of key stress response pathways and triggers specific genes that efficiently alleviate Al stress effects in  P. massoniana . The candidate genes resources generated in this study are of utmost importance for functional characterization and molecular studies aiming at improving Al tolerance in plants.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02719-3.

Identification of candidate genes conferring tolerance to aluminum stress in Pinus massoniana inoculated with ectomycorrhizal fungus