Integrative multi-omics approaches revealed that Asian cultivated rice domestication influenced its symbiotic relationship with arbuscular mycorrhizal fungi

Potential changes in the symbiotic relationship between rice (Oryza sativa) and microorganisms have occurred during the domestication of Asian cultivated rice (O. sativa) from common wild rice (O. rufipogon) and in response to global climate change, along with evolving adaptations to the environment. The potential genes may express differently or dominate the symbiotic relationships between AMF and plants, which may be beneficial in rice breeding. To date, research on this important topic has been limited. In this study, we aimed to examine the symbiotic relationship of common wild rice and Asian cultivated rice species with arbuscular mycorrhizal fungi (AMF). By conducting a comparative metagenomic analysis of the rhizospheres of wild and cultivated rice species, we identified differences in Rhizophagus intraradices-related genes associated with wild and cultivated rice, as well as functional genes of AMF. Furthermore, we obtained root-related genes associated with AMF from transcriptome data of rice roots. Our results collectively suggest that R. intraradices-related genes in the rhizosphere of wild rice may be more conducive to its colonization. Additionally, bacteria from the Nitrosomonadaceae and Nitrospiraceae families identified in the rhizosphere of wild rice exhibited positive correlations with R. intraradices-related genes 1480749 and 1871253, which may indicate that nitrobacteria can enhance the functions of R. intraradicesin association with wild rice. Next, in a case study using comparative transcriptome analysis of root samples obtained from R. intraradices-inoculated wild and cultivated rice plants, we found significantly higher expression levels of the strigolactone pathway-related genes DWARF 3 (D3) and D14 in R. intraradices-inoculated common wild rice than in R. intraradices-inoculated cultivated rice. This study provides a theoretical basis for identifying the effects of domestication on mycorrhizal symbiosis-related genes, which could be promoted in wild rice in the future.