Carotenoid content and root color of cultivated carrot: a candidate-gene association study using an original broad unstructured population

PLoS One. 2015 Jan 23;10(1):e0116674. doi: 10.1371/journal.pone.0116674. eCollection 2015.


Accumulated in large amounts in carrot, carotenoids are an important product quality attribute and therefore a major breeding trait. However, the knowledge of carotenoid accumulation genetic control in this root vegetable is still limited. In order to identify the genetic variants linked to this character, we performed an association mapping study with a candidate gene approach. We developed an original unstructured population with a broad genetic basis to avoid the pitfall of false positive detection due to population stratification. We genotyped 109 SNPs located in 17 candidate genes – mostly carotenoid biosynthesis genes – on 380 individuals, and tested the association with carotenoid contents and color components. Total carotenoids and β-carotene contents were significantly associated with genes zeaxanthin epoxydase (ZEP), phytoene desaturase (PDS) and carotenoid isomerase (CRTISO) while α-carotene was associated with CRTISO and plastid terminal oxidase (PTOX) genes. Color components were associated most significantly with ZEP. Our results suggest the involvement of the couple PDS/PTOX and ZEP in carotenoid accumulation, as the result of the metabolic and catabolic activities respectively. This study brings new insights in the understanding of the carotenoid pathway in non-photosynthetic organs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosynthetic Pathways
  • Carotenoids / analysis
  • Carotenoids / biosynthesis*
  • Daucus carota / anatomy & histology
  • Daucus carota / chemistry*
  • Daucus carota / enzymology*
  • Daucus carota / genetics
  • Genetic Association Studies
  • Oxidoreductases / genetics
  • Plant Proteins / genetics*
  • Plant Roots / chemistry
  • Plant Roots / enzymology
  • Plant Roots / genetics
  • Polymorphism, Single Nucleotide
  • cis-trans-Isomerases / genetics


  • Plant Proteins
  • Carotenoids
  • Oxidoreductases
  • zeaxanthin epoxidase
  • phytoene dehydrogenase
  • cis-trans-Isomerases

Grant support

This work was funded by the French ministry of Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.