Genetic and environmental factors collectively determine plant growth and yield. This study integrated GWAS, MWAS, and mGWAS to analyze 827 foxtail millet cultivars, identifying 257 rhizoplane microbial biomarkers associated with agronomic traits. The study validated microbial-mediated growth effects and uncovered a genotype-microbiota interaction network influencing phenotype plasticity. Results suggest that precision microbiome management could enhance crop yields.