Host metabolites explain microbiome variation between different rice genotypes

作者：Pin Su, Houxiang Kang, Qianze Peng, Weiye Peng, Shu'e Sun, Xiaohua Du, Chi Zhang, Ziling Lei, Lianyang Bai, Qianjun Tang, Yong Liu, Tomislav Cernava, Deyong Zhang · 发表于：Microbiome · 年份：2025 · DOI：10.1186/s40168-025-02181-z · 被引用次数：11 · 研究领域：Plant-Microbe Interactions and Immunity、Plant Gene Expression Analysis、Plant biochemistry and biosynthesis

BACKGROUND: Plants live in close association with microbial communities that support their health and growth. Previous research has indicated that the composition of these communities can differ between genotypes of the same plant species. Host-related factors causing this variation are mostly unknown. Microbiome genes, or M genes in short, are host genes that are involved in shaping the microbiome. We hypothesized that specific M genes are responsible for microbiome variation between rice genotypes and that it is connected to plant metabolites controlled by these genes. RESULTS: Our study was aimed at identifying plant metabolites driving genotype-specific microbiome assembly and establishing a link to host genetics. Targeted metabolite quantification was combined with microbiome profiling of the rice phyllosphere microbiome, association analyses on single-nucleotide polymorphism (SNP) level, and genetic modifications to validate microbiome-shaping effects of the discovered M genes. Targeted metabolite quantifications revealed that phenylpropanoid concentrations in rice leaves can substantially differ among 110 representative genotypes grown under the same, controlled conditions. Redundancy analyses (RDA) showed that these metabolites can explain 35.6% of the variance in their microbiomes. Further verification experiments resulted in the identification of two M genes. OsC4H2 and OsPAL06 are both plant genes with microbiome-shaping effects, mainly via their role in ferulic ac...