Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots

Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high alpha- and beta-carotene orange phenotype. All three genes control high alpha- and beta-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level. This study demonstrates that orange carrot was selected during the Renaissance period, probably in western Europe, through the selection of three recessive genes that increased the provitamin A carotenoid (alpha- and beta-carotene) content.

Automated summary

This study used an improved carrot reference genome and resequencing data from 630 carrot accessions to investigate the domestication and improvement of carrots. The findings suggest that carrot was domesticated during the Early Middle Ages in western Asia to central Asia, and orange carrot was selected during the Renaissance period, possibly in western Europe. The study also identified genes related to circadian clock/flowering and carotenoid accumulation that were under selection during domestication and improvement. Three recessive genes were found to be essential for selecting the high alpha- and beta-carotene orange phenotype. These genes regulate carotenoid accumulation through molecular mechanisms involving the carotenoid biosynthetic pathway, the photosynthetic system, and chloroplast biogenesis. Overall, this study provides insights into the domestication and breeding history of carrots and the genetics of carotenoid accumulation.