ARS | Publication request: Major QTL for Carrot Color are Associated with Carotenoid Biosynthetic Genes and Interact Epistatically in a Domesticated x Wild Carrot Cross

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 20, 2009
Publication Date: November 1, 2009
Citation: Just, B.J., Santos, C.F., Yandell, B.S., Simon, P.W. 2009. Major QTL for Carrot Color are Associated with Carotenoid Biosynthetic Genes and Interact Epistatically in a Domesticated x Wild Carrot Cross. Theoretical and Applied Genetics. 119(7):1155-1169.

Interpretive Summary: One of the most striking differences between the modern cultivated carrot and the wild carrot (also known as Queen Anne’s Lace, QAL) is that the cultivated carrot accumulates high levels of carotenoids in the storage roots giving it its characteristic orange color, while the wild carrot roots accumulate no carotenoid pigments, and consequently are white. It is thought that the first domesticated carotene carrot was yellow in color and that the familiar modern orange carrot, that accumulates beta- and alpha-carotene, was selected through this yellow carrot intermediate within the last 500 years. The genetic control of color due to carotenoid accumulation in carrot roots has been the subject of several research reports but we still know little about the basic biochemistry of carotenoid pigment as it relates to the genetics. There are about 25 enzymes involved in the biosynthesis of carotenoids and in past work we located 23 of them on the genetic map. In past research we also identified all the major genes for carotenoid accumulation. In this research we jointly examined the genetics of these carotenoid biosynthetic enzymes and the carotenoid color genes in an intercross between a cultivated orange carrot and a wild white carrot. We discovered that the two major carrot orange color genes are very close on the genetic map to two carotenoid biosynthetic enzymes. This sets the stage for work to evaluate this relationship more closely. This work is of interest to plant geneticists and biochemists, and since the carrot carotenoids are important for human health, U.S. carrot consumers will also have some interest in our findings.

Technical Abstract: Wild carrot roots are white and do not accumulate pigments while the cultivated carrot is one of the richest sources of carotenoid pigments – mainly provitamin A alpha and beta carotenes. In this study we performed QTL analyses for pigment content on a carotenoid biosynthesis function map based on the F2 generation of a wild white carrot (QAL) x domesticated orange carrot (B493) cross. We found two major interacting loci on linkage groups 2 and 5 controlling a large portion of the variation for carotenoid pigments in carrot roots. These genes correspond to the Y and Y2 genes described over 40 years ago, and they are associated with several carotenoid biosynthetic genes including a carotene hydroxylase, an epoxycarotenoid dioxygenase, and zeaxanthin epoxidase that are candidate genes. The dominant allele at the linkage group 2 QTL is epistatic and it inhibits carotenoid accumulation. When this QTL is homozygous recessive, the major carotenoids that accumulate are either only xanthophylls, when a dominant allele occurs at the linkage group 5 QTL, or both carotenes and xanthophylls, when the linkage group 5 QTL is homozygous recessive. These two genes played a major role in carrot domestication and account for the significant role that modern carrot plays in vitamin A nutrition.