Plant genetics have been shown to play a significant role in shaping the microbiota, yet little work has been done to identify specific loci driving the structure and function of the rhizosphere microbiome. Identifying host genetic elements influencing the assembly or function of the host-associated microbiome could provide us with a novel method to manage and understand our root-associated soils. Here we use the genetic variability that exists within the Zea genus, which comprises an ecologically diverse collection of plant species including domesticated maize and its closest wild relative, teosinte, to understand the relationship between host genetics and structure and function of the rhizosphere microbiome. We have previously found that maize and teosinte assemble their below-ground rhizosphere communities very differently. These microbiome differences manifest themselves in changes in diversity, composition, and rates of microbial N-cycling metabolism. To further dissect the genetic basis of these ancestral microbiome traits, we used teosinte-maize near-isogenic lines (NILs), which allows for the fine mapping of traits to specific genetic loci in the plant genome. NILs were grown in the field setting and greenhouse in a randomized complete block design and were characterized for microbiomes assembly, potential nitrogen cycling, and root metabolomics.
Results/Conclusions
From this Maize-Teosinte NIL experimental population, we identified 13 candidate NILs that altered the composition of the microbiome in the root zone. These candidate NILs vary in their degree of influence on the microbial community. Three of these introgressions significantly altered the rhizosphere microbial community composition (P<0.05). Functionally, we identified five NILs that altered the microbiome N-cycling activity (P<0.05). Quantitative trait loci analysis of these functionally important genetic introgressions showed that they contain gene pathways important in secondary metabolite biosynthesis. Ongoing metabolomic screening of root tissue is underway to confirm these results. Together these findings, begin to show that specific plant genetic loci play a mechanistic role in altering the function of the rhizosphere microbiome. This understanding is important as it provides breeders with a novel method by which to manage the function of our agroecosystems and connects different scales of biological understanding.