26Understanding the factors that influence the outcome of crop interactions with microbes is key to 27 managing crop diseases and improving yield. While the composition, structure and functional profile of 28 crop microbial communities are shaped by complex interactions between the host, microbes and the 29 environment, the relative contribution of each of these factors is mostly unknown. Here, we profiled the 30 community composition of bacteria across leaves of 3,024 rice (Oryza sativa) accessions from field trials 31 in China and the Philippines using metagenomics. Despite significant differences in diversity between 32 environments, the structure and metabolic profiles of the microbiome appear to be conserved, suggesting 33 that microbiomes converge onto core functions. Furthermore, co-occurrence analysis identified microbial 34 hubs that regulate the network structure of the microbiome. We identified rice genomic regions controlling 35 the abundance of these hubs, enriched for processes involved in stress responses and carbohydrate 36 metabolism. We functionally validated the importance of these processes, finding that abundance of hub 37 taxa was different in rice mutants with altered cellulose and salicylate accumulation, two major 38 metabolites at the host-microbe interactions interface. By identifying key host genomic regions, host traits 39 and hub microbes that govern microbiome composition, our study opens the door to designing future 40 cropping systems. 41 42

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