Host metabolites explain microbiome variation between different rice genotypes

Area of Science:

• Plant science
• Microbiome research
• Genetics

Background:

• Plant health relies on associated microbial communities, with variations observed between plant genotypes.
• Host genetic factors influencing these microbiome differences are largely unknown.
• Microbiome genes (M genes) are host genes that shape plant-associated microbial communities.

Purpose of the Study:

• To identify plant metabolites driving genotype-specific microbiome assembly in rice.
• To establish a link between host genetics and microbiome variation.
• To validate the microbiome-shaping effects of identified M genes.

Main Methods:

• Targeted metabolite quantification in rice leaves across 110 genotypes.
• Microbiome profiling of the rice phyllosphere.
• Association analyses using single-nucleotide polymorphism (SNP) data and genetic modifications.

Main Results:

• Phenylpropanoid concentrations varied significantly among rice genotypes, explaining 35.6% of microbiome variance.
• Two M genes, OsC4H2 and OsPAL06, were identified with microbiome-shaping effects, primarily through ferulic acid biosynthesis.
• Gene mutation experiments confirmed distinct bacterial groups' responsiveness to these M genes.

Conclusions:

• Host genetics significantly influence plant microbiome composition through specific M genes.
• Understanding these genetic controls enables microbiome engineering for improved plant health.
• This knowledge supports targeted plant breeding strategies for microbiome optimization.