QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots

Mol Genet Genomics. 2002 Sep;268(1):122-9. doi: 10.1007/s00438-002-0735-9. Epub 2002 Aug 9.


QTLs associated with products of the carotenoid pathway, including lycopene and the provitamin A carotenes alpha- and beta-carotene, were investigated in two unrelated F(2) carrot populations, derived from crosses between orange cultivated B493 and white wild QAL (Population 1), and orange cultivated Brasilia and dark-orange cultivated HCM (Population 2). The mapping populations of 160 and 180 individuals, respectively, were analyzed with single-marker and interval-mapping statistical approaches, using coupling linkage maps for each parent. Single markers were selected for further analysis based on the Wilcoxon sum-rank non-parametric test. Interval mapping performed with Population 2 detected four, eight, three, one and five putative QTLs associated with accumulation of xi-carotene, alpha-carotene, beta-carotene, lycopene and phytoene, respectively. Among these, the major QTLs explained 13.0%, 10.2%, 13.0%, 7.2% and 10.2% of total phenotypic variation. In Population 1 single-marker analysis identified loci explaining up to 13.8%, 6.8%, 19.3%, 5.7%, and 17.5%, respectively, of total phenotypic variation for these same carotenoids. Overall analysis demonstrated clustering of these QTLs associated with the carotenoid pathway: the AFLP loci AACCAT178-Q and AAGCAG233-Q, on linkage group 5, explained 17.8%, 22.8% and 23.5% of total phenotypic variation for zeta-carotene, phytoene and beta-carotene in Population 1. Two major clusters of QTLs, with LOD scores greater than 1.8, mapped to intervals no larger than 2 cM for zeta-carotene, beta-carotene, alpha-carotene and lycopene on linkage group 3, and for zeta-carotene and phytoene on linkage group 9, and these explained 3.7% to 13.0% of variation for each carotenoid product. Thus, these results suggest that clustering of related pathway loci is favored during evolution, since closely linked "pathway mates" are not easily separated by recombination.

MeSH terms

  • Carotenoids / biosynthesis
  • Carotenoids / metabolism*
  • Chromosome Mapping
  • Crosses, Genetic
  • DNA, Plant / genetics
  • Daucus carota / genetics*
  • Daucus carota / metabolism
  • Genetic Linkage
  • Likelihood Functions
  • Lycopene
  • Multigene Family / genetics*
  • Plant Roots / genetics
  • Plant Roots / metabolism*
  • Quantitative Trait Loci / genetics*
  • Vitamin A / biosynthesis*
  • Vitamin A / metabolism


  • DNA, Plant
  • Vitamin A
  • Carotenoids
  • Lycopene