Genetic mapping of carotenoid pathway structural genes and major gene QTLs for carotenoid accumulation in wild and domesticated carrot (Daucus carota L.)

Carrots are an excellent source of provitamin A carotenoids in the human diet and these pigments impart the familiar orange root color. Since carotenoids are an important trait for breeders as well as nutritionists, an understanding of the genetics and biochemistry of carotenoids is desirable. An attempt was made to identify putative genes coding for enzymes in the carotenoid biosynthetic pathway in carrot and to place them on a carrot genetic linkage map. Sixteen new putative genes were identified in the carrot genome, for a total of 24 genes. Of these, 22 were mapped in a B493 x QAL F2 population on eight of the nine linkage groups in carrot. To determine whether polymorphism in any of these genes was responsible for differences in carotenoid accumulation between wild white and domesticated orange carrot, a QTL analysis was performed for major intermediates in the carotenoid pathway and for total carotenes using the map with carotenoid biosynthetic genes. Two large effect QTLs were detected and demonstrated evidence for interaction explaining a large portion of the variation for carotenoid accumulation between wild and domesticated carrot (∼57% of the variation in total carotenes). One of these loci mapped near the putative zeaxanthin epoxidase (ZEP) gene on linkage group 5 and another mapped near a putative epsilon ring carotene hydroxylase (CHXE) on linkage group 2. The QTL on linkage group 5 maps to the same region as the well-characterized Y2 gene and its effects are consistent with its identity as Y2. The QTL on linkage group 2 was examined in F3, F4 and test cross generations. This locus may be allelic to the Y locus. Another locus studied in F 3 and F4 populations maps to linkage group 4 and has a lesser effect than Y. Lastly, we examined expression of the putative biosynthetic enzymes and attempted to obtain full-length cDNA clones for all expressed genes. No obvious and consistent differences in expression patterns were observed between different colored carrots. However, expression was detected for 20 genes and full-length cDNAs were obtained from 18 genes.