Patterns and Consequences of Breeding-Induced Metagenome Variation in Maize

Food security in a changing world requires crops that perform well without the unsustainably high inputs of water and chemicals that enabled past breeding successes. The crop metagenome—the combined genetic content of all plant-associated microorganisms—is a vast untapped reservoir of functional diversity with great potential for agricultural applications, because it dramatically affects the health and productivity of the host plant. The metagenome is partially heritable, but it is unknown how host genetic changes during breeding affect metagenome composition and function. This project addresses the following questions: (1) Is metagenome composition of F1 hybrids intermediate to that of their parent lines, or does it exhibit heterosis like many other maize traits? (2) Does recurrent selection—which alters allele frequencies in genes underlying both target and non-target traits—have side-effects on metagenome content? (3) Does introgression of loci for broad-spectrum resistance to multiple pathogens affect colonization by nonpathogenic microbes and the resulting metagenome?

Here I describe experiments to quantify patterns and consequences of breeding-induced metagenome variation in maize. Field-grown plants with contrasting genotypes from active maize breeding programs will be sampled and sequenced, using both amplicon-based microbiome censuses and whole-metagenome shotgun sequencing. Root-associated microbial communities will be collected from all maize lines and re-applied as inocula in follow-up experiments to test for effects of breeding-induced metagenome variation on plant vigor and disease resistance. Together, answers to these questions will reveal the connections between plant genomic variation, microbiome diversity, and crop health in the contexts of hybridization, artificial selection, and introgression.