Additional file 3 of Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

Additional file 3: Table S1. List of 3 K-RGP rice accessions with number of reads that did not map to the rice genomes (unmapped reads). Table S2. Phyla and genera composition of the 3 K RGP microbiome. Table S3. Significant genera that contribute to the differences between accessions grown in China and accessions grown in Philippines. Table S4. Quantitative PCR validation of metagenomic analysis using 17 rice accessions from the 3 K-RGP project. The table indicate the genera used for the experiments, followed by the primer sequences, the reference for the primers, the qPCR results (delta Ct and standard deviation). Then the list of the 17 accessions and their groups are indicated. Table S5. Co-abundance network values for the most abundant genera in the 3KRGP microbiome. Table S6. Co-abundance network modules with the most connected microbes. Table S7. Metabolic pathways predicted by Vikodak based on KEGG levels 1 and 3. Table S8. Significant signals from the genome wide association analysis (GWAS). Table S9. Description of haplotype blocks for each significant SNP, number of associated candidate genes and the QTLs that match to the same region.