Plant Material
We used a population of recombinant inbred lines (RILs) derived from a cross between P. hallii var. hallii (HAL2 genotype) andP. hallii var. filipes (FIL2 genotype) to evaluate the genetic basis of plant-microbiome interactions. A single F1 hybrid was used to generate a F2population which was bred by single seed descent to the F7 generation (Khasanova et al. 2019). Parents have full genome assemblies that are publicly available (https://phytozome-next.jgi.doe.gov/; Lovell et al. , 2018). The RIL population linkage map was constructed by shallow whole-genome resequencing and is congruent with the order of the physical genome. Seeds of 293 F7RILs and parents were sterilized, germinated, transplanted into treatment pots in a greenhouse located at the University of Texas at Austin (16-h days at 500 μE m −2 s−1, 28°C; 8-h nights at 24°C; full protocol in Appendix S1).