The soil microbiome and its interaction with plants via the root system plays an important role in plant growth, survival and reproduction. Plants and microbes have co-evolved together and this co-evolution has been driven by the shared interactions between them. Microbial interactions may also play a role in the process of ecotype formation, where populations diverge across many traits and exhibit different niche characteristics. Plant associated microbiomes impact root phenotypic traits, can increase nutrient acquisition, provide indirect impacts on shoot traits and promote tolerance to abiotic and biotic stress. The objective of this study is to use a quantitative genetics framework to map genomic regions associated with plant-microbiome interactions in order to understand the impact of native soil microbiomes on root traits and plant performance.
Panicum hallii is an emerging model system for C4 perennial grasses, including the important biofuel crop switchgrass (P. virgatum). We produced an intercross between individuals of the xeric and mesic ecotypes of P. hallii and utilized a single seed decent method to generate a population of recombinant inbred lines (RILs) at the F7 generation. We subsequently constructed a genetic map based on whole genome re-sequencing of the population. Native soil was collected from the natural habitats of each of the RIL parent ecotypes and used to inoculate autoclaved greenhouse soil. 374 RILs were grown in the presence and absence of both native microbiomes and in control soils comprised of greenhouse soil inoculated with autoclaved native soils. We conducted extensive phenotyping of root and shoot traits and employed a quantitative genetic approach to analyze the data.
Results/Conclusions
We identified several genomic ‘hotspots’ across all treatments which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. We also identified root and shoot QTL specifically associated with the presence or absence of introduced microbiomes. This indicates that plant root microbiome interactions can shape root architecture and impact plant performance.