P-269 - A three-year genome-wide association study reveals the temporal interplay between host genetics and the microbiota in rice

Plant genetics and environmental factors collectively shape the assembly of the root microbiome. Unraveling the genetic basis of host plant–microbiome interactions is critical for translating microbiome insights into crop breeding. Here, we conducted microbiome genome-wide association studies over three years using a panel of ~150 accessions from a rice core germplasm collection. 16S rRNA gene-based profiling of rice root samples revealed diverse bacterial compositions between different cultivars. We found that environmental shifts across years drove ~75% of the variations of the root microbiota. Host genetics explained 3.63%-12.04% of the root microbial variation annually, with 23-52 highly abundant heritable bacterial taxa identified per year. mGWAS identified 2,846 lead SNPs significantly associated with 778 OTUs with relative abundance >10^-4 and prevalence > 50% (P < 10^-6). Notably, 3,359, 1,832 and 1,816 associations were detected in each respective year, yet none were consistently detected across all three years. GO enrichment analysis indicated that candidate genes are associated with various functions, including phosphate metabolism, kinase activity, nucleotide binding, and cell membrane surface receptor signal transduction. Our findings highlight the high dynamics of rice root microbiome assembly in paddy fields and identify candidate genes temporally associated with root bacterial diversity.