Exploiting Lotus japonicus natural variation

Plant root microbiota is known to play a crucial role in plant growth and health. The host plant can recruit commensal or beneficial bacteria that could directly promote plant growth, create good environmental conditions or help to protect against pathogen infection. Manipulating this root microbiota would help to improve sustainable crop management in the future. By using a Japanese collection of Lotus japonicus accessions, we focus on natural variation to elucidate the genetic mechanisms of microbiome recruitment. Here, we used a synthetic community of 107 bacterial strains isolated from Lotus roots to inoculate 165 diverse Lotus accessions and evaluate the rhizosphere microbiome structure thanks to amplicon sequencing. By using the relative abundances data, we performed GWAS that allowed identifying candidate genes associated with changes in the microbiome at a strain level but also at a more general microbiome structure level. The statistical power of this study and the fact that some of these candidates have been found many times by using the abundances of different strains in different replicates, indicates that we might have discovered important plant genes involved in rhizosphere microbiome assembly. The next step of this project would be the functional validation of these candidates by characterizing the differences in microbiome structure with LORE1 insertion mutants compared to Wild-type plants. Among these candidates, the ones showing the most interesting phenotypes would be selected for further characterizations.