Integrative multi-omics approaches reveal that Asian cultivated rice domestication influences 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 (Oryza 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 arbuscular mycorrhizal fungi (AMF) and plants, which may be beneficial to rice breeding. To date, research on this important topic has been limited. In this study, we aimed to examine the symbiotic relationships of Asian common wild and cultivated rice species with 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 with protein identifiers 1480749 and 1871253, which may indicate that nitrobacteria can enhance the functions of R. intraradices in 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 DWARF3 (D3) and DWARF14 (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.},