Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency.

Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.