DOI: 10.5061/dryad.8sm01
title: Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community

description: 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.
description: GWAS Results,
 PCAResults 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.tgzGWAS Results, CCAResults 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.tgzGWAS Results, DCAResults 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.tgzGWAS 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.tgzGWAS Results, Abundance (Sqrt(x)) of Individual OTUsThe 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.tgzGWAS 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