High-Resolution Mapping of Root and Leaf Anthocyanin Pigmentation QTL in Carrot

Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. We scored root color visually and quantified root anthocyanin pigments by high performance liquid chromatography in segregating generations of a mapping population, mapped quantitative loci for these traits onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color. All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F₂ population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635 cM with a 1.3 cM map resolution. A total of 15 QTL mapped to six chromosomes. A single dominant gene conditioning anthocyanin acylation was identified and mapped. Comparative mapping with other carrot populations segregating for purple color indicated that genetic control of anthocyanin pigmentation in this species is controlled by at least three genes, in contrast to monogenic control. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for root pigment content, largely condition anthocyanin accumulation in roots and leaves. The loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.