ROOMIE1 controls rhizobiome assembly in Lotus japonicus and shows a genomic signature distinct from climate‐associated loci

How plant genomes accommodate selective pressures across spatial and temporal scales remains poorly understood. Here, we address this by comparing the population-genomic signatures of root microbiome- and climate-associated loci in a natural Lotus japonicus population. We inoculated 155 L. japonicus accessions with a synthetic community of 107 bacterial isolates and performed genome-wide association analyses of rhizosphere microbiome traits. We then carried out functional validation, testing effects of mutations and natural allelic variation, and compared population-genomic characteristics of microbiome-associated and climate-associated loci. We identified 355 significant quantitative trait loci associated with rhizosphere microbiome variation. Microbiome-associated loci showed heterogeneous genomic signatures. One subset displayed strong regional differentiation and near fixation of specific haplotypes, whereas another showed low differentiation, and maintenance of multiple haplotypes within populations. The latter pattern was exemplified by ROOT MICROBIOME ESTABLISHMENT 1 (ROOMIE1). Disruption of ROOMIE1 reproducibly altered rhizosphere microbiome composition in both synthetic communities and native soil, whereas natural ROOMIE1 haplotypes were associated with microbiome differences among closely related accessions. Our findings reveal that microbiome-associated loci can display population-genomic signatures that sharply contrast with those at climate-associated loci, with ROOMIE1 representing a host gene that controls rhizosphere microbiome composition and shows standing haplotype variation at a local scale.