Identifying the factors that influence the outcome of host–microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.
GWAS Results, PCA
Results from GWAS of eigenvectors (PCs) 1-5, after PCA of the bacterial and (separately) the fungal community. This tarball includes 'reports' (e.g. the top SNPs after GWAS), image files (manhattan plots), and the top GO-terms enriched in these GWAS results. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
pca.tgz
GWAS Results, CCA
Results from GWAS of eigenvectors (CCAs) 1-5, after CCA of the bacterial and (separately) the fungal community. This tarball includes 'reports' (e.g. the top SNPs after GWAS), image files (manhattan plots), and the top GO-terms enriched in these GWAS results. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
cca.tgz
GWAS Results, DCA
Results from GWAS of eigenvectors (DCAs) 1-4, after DCA of the bacterial and (separately) the fungal community. This tarball includes 'reports' (e.g. the top SNPs after GWAS), image files (manhattan plots), and the top GO-terms enriched in these GWAS results. The Methods section of the manuscript describes the procedure. Please note that 'decorana' (vegan's function, which was used for DCA) only returns 4 axes. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
dca.tgz
GWAS Results, Presence-Absence (0/1) of Individual OTUs.
The presence or absence (0/1) of individual OTUs were used as phenotypes in GWAS. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
pres.tgz
GWAS Results, Abundance (Sqrt(x)) of Individual OTUs
The square-root transformed abundances of individual OTUs were used as phenotypes in GWAS. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
sqrt.tgz
GWAS Results, Individual OTUs (results from P/A and Sqrt(x) combined)
The presence vs. absence (0/1) of individual OTUs were used as phenotypes in GWAS. In separate analyses, the abundance (sqrt(x)) of individual OTUs were also used as phenotypes. These results (p-values) were combined using Brown's (1975) approach. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
combined.tgz
