Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Here, taxonomic and (meta)genomic features of the rhizosphere microbiome were mapped as quantitative traits of a tomato recombinant inbred line population. The amplicon-based approach identified QTLs to more taxa, whereas the metagenomics-based approach identified QTL regions with significantly smaller 95% confidence intervals. Gene content analysis of prioritized tomato QTLs suggested a genetic basis for differential recruitment of rhizobacterial lineages in the tomato rhizosphere. Within the rhizosphere, metagenome-assembled genomes of rhizobacterial lineages identified microbial genes related to the metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins linked to QTL regions. By combining microbiomics and quantitative plant genetics, our results pinpoint the reciprocal plant and microbial candidate traits associated with microbiome assembly, paving the way for integrating the microbiome into plant breeding programs.