Supplementary material 2 122_2019_3366_MOESM2_ESM.xlsx

List of tables included in this file
Supplementary Table S1. Characteristics of the plant materials and sequencing libraries used for transcriptome (RNA-seq) analysis, and number of reads obtained for each sample
Supplementary Table S2. Normalization factors for pair-wise transcriptome comparison
Supplementary Table S3: Observed phenotypic frequencies of purple pigmentation in the root phloem (A) and xylem (B), and in leaf petioles (C), in F2, and F4 carrot families
Supplementary Table S4. Concentration of individual and combined anthocyanin pigments in purple root phloem and xylem tissues of population 3242 (A) and concentration of individual and combined anthocyanin pigments in roots of population 5171 (B)
Supplementary Table S5. Summary of QTL for individual and combined anthocyanin pigments in the root phloem of population 3242 obtained using the multiple imputation mapping method
Supplementary Table S6. Summary of QTL for individual and combined anthocyanin pigments in the root phloem of population 3242 obtained using the Haley Knott regression method
Supplementary Table S7. Marker allelic interactions for phloem anthocyanin QTL on chromosome 3 that revealed significant interactions
Supplementary Table S8. Summary of QTL for individual and combined anthocyanin pigments in purple roots of population 5171, detected with the Haley Knott regression mapping method
Supplementary Table S9. Phenotypic information for carrot root and petioles color, and marker genotypes for the F2 samples used in QTL mapping
Supplementary Table S10. Phenotypic information for carrot root and petioles color, and marker genotypes for the F4 samples used in QTL mapping
Supplementary Table S11. Carrot predicted peptides annotated as structural genes involved in the flavonoid and anthocyanin biosynthetic pathways
Supplementary Table S12. List of annotated genes in the P1 and P3 regions of chromosome 3 harboring co-localized QTL for tissue-specific anthocyanin pigments. Subject descriptions are the top Blastp hits in Swiss-Prot
Supplementary Table S13. List of MYB, bHLH and WD40 transcription factors identified within the P1 and P3 regions of chromosome 3
Supplementary Table S14. MYB, bHLH and WD40 transcription factors (TF) used for phylogenetic analyses
Supplementary Table 15. Differentially expressed genes (DEGs) detected in pairwise transcriptome (RNA-Seq) comparisons between purple and non-purple carrot roots, and among purple roots with different anthocyanin concentration
Supplementary Table S16. Differentially expressed genes (DEGs) in the P1 and P3 regions of CHR 3 found in all 15 of the purple versus non-purple root transcriptome comparisons
Supplementary Table 17. Expression analysis of candidate MYB genes (i.e., MYBs in the P1 and P3 regions of CHR 3 and phylogenetically-related to MYBs from other species known to be involved in anthocyanin biosynthesis) in pairwise transcriptome comparisons between purple and non-purple carrot roots, and among purple roots with different anthocyanin concentration
Suplementary Table S18. Differentially expressed genes (DEGs) in the P1 and P3 regions of CHR 3 resulting from pair-wise transcriptome comparisons among dark purple (dP), medium purple (mP), and pale purple (pP) roots, containing high, intermediate, and low anthocyanin concentration, respectively.
Supplementary Table S19. Genes used for phylogenetic analysis of CYP450 enzymes