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.