Figure 4: Phenotypes, candidate genes, and transcriptome changes associated with carotenoid accumulation in carrot roots.

(a) Phenotypes associated with the Y locus, including pale orange (pOr), dark orange (dOr), yellow (Y), and white (W) roots, from the indicated populations. (b) Previously published genetic map and location of the Y locus⁴¹. (c) Carrot chromosome 5 and the molecular markers used for fine-mapping of the Y locus. The genotypes of the 76-kb region in recombinant individuals are illustrated (Supplementary Fig. 25). Het, heterozygous. (d) The fine-mapped region controlling the Y locus. Numbers represent the eight genes predicted in this region. Gene 7, DCAR_032551, was the only gene differentially expressed (upregulated) in RNA-seq analysis of yellow versus white and dark orange versus pale orange samples. Below are all the nonsynonymous SNPs (for example, G>A) and insertions (ins) identified in the four genes located in the 65-kb haplotype block associated with the Y locus in the resequencing samples (Supplementary Table 40). The number of accessions with each haplotype block classification (I–III; Supplementary Table 17) is given. The DCAR_032551 y^a variant harbors a 212-nt insertion in the second exon, and the y^b variant harbors a 1-nt insertion in the second exon. Het, heterozygous. (e,f) Nucleotide diversity (π) estimated in wild (blue) and cultivated (orange) carrots (e) and the top 1% of F_ST values (blue) (f) in the 75-kb region (gray shading) of carrot chromosome 5. (g,h) Patterns of LD in wild (g) and cultivated (h) carrots. Red and white spots indicate regions of strong (r² = 1) and weak (r² = 0) LD, respectively. The gray bar indicates the position of the 75-kb fine-mapped region harboring the Y candidate gene.