Additional file 2: Table S1. The list of collected 292 varieties. Table S2. Classification of 292 apple accessions. Table S3. Statistical results of heredity and variation. Table S4. Scheduled MRM transitions for widely targeted metabolite analysis in apple flesh. Table S5. Different metabolites identified between M. sieversii and heirloom groups. Table S6. Different metabolites identified between heirloom and cultivar groups. Table S7. Different metabolites identified among “Ralls Janet” and “Golden Delicious” series. Table S8. Different metabolites identified between low- and high-weight groups. Table S9. All significant SNPs for all apple metabolites Table S10. Candidate genes for tannins, lipids, SA, and ABA identified by GWAS. Table S11. Primers used in this study