Additional file 1 Table S1. The genome ploidy level analysis of cultivated oil-camellia and wild species close to the oil-Camellia. Table S2. The hybrid assembly statistics of the sequenced CON genome. Table S3. Summary of repetitive sequence identification. Table S4. Summary of Non-coding RNA gene annotation. Table S5. The assessment of gene models of the CON genome. Table S6. Summary of gene function annotation using various databases. Table S7. Summary of BUSCOs genome assessment results. Table S8. Statistics of data production by ddRAD sequencing for each individual in F1 population. Table S9. A summary of statistics of all SNP markers types in linkage population. Table S10. Features of the 15 linkage groups (LG) in linkage map of C. oleifera. Table S11. Origin of the 221 accessions in the association population and summary of their RNAseq data. Table S12. Details of eight important oil traits in mature kernel of C. oleifera all accessions for three consecutive years (2013, 2014 and 2015). Table S13. Analysis of variance for eight oil traits in the association population of C. oleifera. Table S14. Statistics of SNPs of C. oleifera association population in this study. Table S15. Statistics of InDels of C. oleifera association population in this study. Table S16. Mean of fruit traits of C. oleifera association population. Table S17. The enriched GO terms based on the genes from selective sweep analysis. Table S18. Loci significantly associated with oil traits in GWAS. Table S19. The key candidate genes mined by qGWAS in C. oleifera association population. Table S20. Summary of the significantly enriched KEGG pathways of the genes with cis-eQTLs, trans-eQTLs targeted genes and genes covered the trans-eQTLs. Table S21. The summary of Sanger sequencing validation of SNPs identified by the RNA-seq analysis. Table S22. The first ten components in PCA results of association population. Table S23. Description of the Sanger sequencing primers used in our studies. Table S24. Description of the Real-time quantitative PCR primers used in our studies.