Wild Rice Gene Restores a Nitrogen-Helping Root Microbiome in Cultivated Rice

A gene carried predominantly by wild rice can help cultivated rice recruit root bacteria associated with nitrogen uptake, according to a peer-reviewed study published September 30 in Nature Microbiology. The researchers identified the receptor-like kinase gene OsRLK and showed that restoring its activity in cultivated rice changed its interaction with Acinetobacter bacteria, increased nitrogen-related functions and improved several yield-related traits in field tests.

The work addresses a hidden consequence of crop domestication. Breeding has transformed plant architecture, maturity, grain quality and yield, but selection above ground can also alter the chemistry and genetics that shape microbial communities around roots. The study’s central proposition is that some beneficial partnerships lost during domestication can be deliberately recovered through breeding—a process the authors call microbiome re-domestication.

The researchers crossed cultivated rice with its wild relative Oryza rufipogon and followed root-associated bacteria through two recombinant inbred-line populations. They combined field experiments, microbiome profiling, quantitative-trait-locus mapping, population genomics and gene-expression analysis. That process produced 113 candidate plant genes associated with microbial groups, narrowing the focus to OsRLK on chromosome 4.

Natural variation strengthened the genetic link. The team compared the OsRLK region across 382 rice accessions and sequenced the coding region in 105 of them—33 wild and 72 cultivated. They identified 28 single-nucleotide changes and two insertions or deletions that formed three haplotypes. The main wild-rice version was associated with greater abundance of specific Acinetobacter variants than the principal cultivated-rice version.

Functional tests moved the result beyond statistical association. The researchers created cultivated-rice lines that overexpressed OsRLK and wild-rice lines in which the gene was knocked out. They then inoculated plants with a synthetic Acinetobacter community. Total plant nitrogen, dry biomass, abundance of the bacteria, the nitrogen-fixation marker nifH and nitrogenase protein were all higher in the OsRLK-overexpressing or wild-rice combinations than in the cultivated wild type and knockout lines under the live-microbe treatment.

The controls are important. When the synthetic bacterial community was heat-killed, the differences did not persist, supporting the interpretation that OsRLK works through a living plant–microbe interaction rather than simply changing growth on its own. In field trials, OsRLK-overexpressing lines recorded significant improvements in effective panicle number, seed-setting rate, thousand-grain weight and grain yield per plant. Panicle length and grain dimensions did not change significantly.

The result is not yet a commercial fertiliser-reduction claim. The published work used experimental transgenic lines, controlled inoculations and defined microbial communities, and the article reports statistically significant yield traits rather than a broadly validated farm-scale yield advantage. Multi-location and multi-season trials would be needed to test stability across soils, climates, management systems and naturally variable microbiomes. Regulators and breeders would also need to determine the most practical route for transferring the useful allele.

Even so, the study establishes a more precise target for microbiome-guided crop improvement. Instead of applying a microbial product and hoping it colonises consistently, breeders may be able to select plant genes that actively recruit and support useful organisms already adapted to the root environment. If the effect proves durable in diverse production systems, wild-crop genetics could become a route to stronger nitrogen-use efficiency without treating the soil microbiome as a separate input.