The Effect of Host Genetics on Maize-Microbiome Interactions.

A major goal in current microbiome research is to determine the extent to which a host organism can shape its own microbiome. This is especially true in crop science, where the answer will determine whether crop-microbe interactions are better addressed through breeding, management, or some combination of the two. We address this problem in maize by looking at the host influence on both rhizosphere (root) and phyllosphere (leaf) microbiome communities. These two communities show very different makeups: the rhizosphere is highly complex, while the phyllsophere is dominated by <20 bacterial taxa. Broad- and narrow-sense heritability analyses show that a subset of microbes are moderately heritable (heritability of 0.3-0.6), while the majority show little effect of the maize genotype. We identify genetic regions implicated in host control of the microbiome, and we show that the environment is probably the major driver across both of these communities. Stochastic processes may also play a strong role in community assembly, especially in the phyllosphere. Taken together, these results indicate that the maize host exerts only partial control over the makeup of its rhizosphere and phyllosphere communities. More work needs to be done to determine to what extent these communities affect their host plant, and determine if and how manipulating them can benefit agriculture.