Additional file 2 of Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites

Additional file 2: Fig. S1. Differentially expressed genes (DEGs) and enrichment analysis. Heat map for DEGs between the PIM and CER groups (A), as well as the CER and BIG groups (B). The Gene ontology (GO) enrichment analysis for DEGs between the PIM and CER groups (C), as well as the CER and BIG groups (D). The KEGG pathway enrichment analysis for DEGs between the PIM and CER groups (E), as well as the CER and BIG groups (F). Fig. S2. Local Manhattan plot (A) and distribution of nucleotide diversity (𝜋) of the PIM, CER, BIG groups for fw11.3 in chromosome 11 (B). Two-Mb zoom of single marker (-log10) P value for GWAS and 100-kb sliding windows GWAS on fruit weight, and the green bars above the chromosomes denote the identified improvement sweeps by EigenGWAS. Fig. S3. GWAS on SIFM0533 and SIFM1279 during domestication, and SIFM0104, SIFM0123, SIFM0154, SIFM0155, SIFM0166, SIFM0656 and SIFM1279 during improvement. Red arrows indicate those significant association signals located in domestication/improvement sweeps using EigenGWAS or 𝜋. Besides these polyphenols, in Supplementary Fig. 4, SIFM0600 were analyzed during domestication and improvement, respectively. Fig. S4. GWAS on DGPC acid. Single marker (-log10) P value for GWAS on DGPC acid during domestication (A) and improvement (B), respectively. The horizontal axis shows chromosome of tomato, while the vertical axis indicates -log10 transformed observed P value. Fig. S5. A genetic region under improvement across the CER and BIG groups for DGPC acid. A Manhattan plot of GWAS on DGPC acid across all chromosome, averaged over 100-kb windows during improvement. Color-highlighted regions indicate peaks found in both the GWAS and EigenGWAS analyses. B EigenGWAS P values in relation to DGPC acid GWAS P values averaged over 100-kb windows. Green dots indicate those windows in the top 1% from GWAS, blue dots indicate those windows above the threshold of EigenGWAS, and purple dots correspond with the highlighted regions in (A). Fig. S6. Heatmap for those DEGs in the selected sweeps satisfy the EigenGWAS and GWAS in low and high content of DGPC acid during improvement. Fig. S7. GWAS on TSPM. Single marker (-log10) P value for GWAS on TSPM during domestication (A) and improvement (B), respectively. The horizontal axis shows chromosome of tomato, while the vertical axis indicates -log10 transformed observed P values. Fig. S8. Spearman's rank correlation coefficient between fruit weight and TSPM. The y axis (TSPM content) and x axis (fruit weight) were log2 transformed, respectively. Lines and shaded areas are fitted values and 95% confidence limits from general linear models.