Carotenoids are compounds playing an essential role in human health, preventing disease thanks to their antioxidant capacity, but also as pro-vitamin A precursors. As human cannot synthesize carotenoid, they have to eat a dietary of plants to provide such compounds. Carrot is one of the most important vegetable in the world, and a critical source of carotenoid as a large amount is accumulated in the root. Moreover carrot genetic resources exhibit a large range of colours and carotenoid content patterns. Carotenoid biosynthesis is today well established and genes encoding carotenoid enzymes have been characterized in many species.

The genetic determinism of carotenoid content in carrot roots has been studied, mainly by linkage mapping. As QTLs might be population-specific, association mapping has emerged in the last decade as an alternative to linkage analysis to dissect the basis of quantitative traits in plants.

However, the diversity in cultivated carrot is structured depending on the geographical origin, both for molecular markers and carotenoid content, which might lead to false associations. In order to overcome this risk, we used a broad unstructured population to perform an association mapping study for carrot root carotenoid content with a candidate gene approach. Association mapping targeting candidate genes brings new insights for carotenoid content and colour in carrot.