Additional file 3: of Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

Figure S1. Genetic diversity of the 480 peach accessions. Figure S2. Manhattan plot and QQ plot of genome-wide association studies on seven important agronomic traits. Figure S3. A candidate 70.5-kb deletion underlying fruit texture. Figure S4. Phenetic neighbor-joining tree of 480 peach accessions constructed using PHYLIP with 100 bootstrap replicates. Figure S5. Population structure of the 480 peach accessions. Figure S6. Phenotypes and nucleotide diversity changes during peach improvement and domestication. Figure S7. Genome-wide association studies (GWAS) of SSC and fruit weight. Figure S8. Regional LD decay measured by R2 at the 20.0–30.0-Mb region of chromosome 2. Figure S9. Total organic acids in domesticated peaches and wild relatives. Figure S10. Genome-wide association study of total phenolic content for peach. Figure S11. Expression profile of a sugar transport gene, Prupe.4G037800, during fruit development in peach. Figure S12. A candidate gene for SSC associated with increase of fruit taste during domestication. Figure S13. Distribution of chilling requirement in 371 peach accessions. Figure S14. Manhattan plot (left) and QQ plot (right) of GWAS for chilling requirement (CR) by classifying accessions into low CR and non-low CR. Figure S15. Comparison of flowering times between Arabidopsis overexpressing of peach SVP gene (OE) and the wild type (WT) Arabidopsis. Figure S16. A PCR-based marker for low CR peach identification based on the results of CR GWAS. Figure S17. Comparison of improvement sweeps between eastern and western improved groups. Figure S18. Shared and private SVs among three callers. Figure S19. Distribution of genotype missing rate for 480 peach accessions. Figure S20. Demographic model for peach domestication and spread. Figure S21. Shared domestication and improvement sweeps identified by ROD and XP-CLR methods. (PDF 2514 kb)