Genetic determinants of switchgrass- root-associated microbiota in field sites spanning its natural range

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environ-mental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switch -grass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composi-tion; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local geno-types preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 micro-bial strains and found an enrichment of genes involved in immune responses, signaling pathways, and sec-ondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manip-ulating beneficial microbial associations via host genetics.

Automated summary

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition. This study characterized the root microbiota of switchgrass in its native range and found that field location is the primary determinant of microbiome composition. They also identified loci impacting the abundance of microbial strains and found a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota.