Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F2 populations

Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F-2 populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the alpha- and beta-carotene contents and a chromoplast-specific lycopene beta-cyclase (CYC-B) gene for the beta/alpha carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.

Automated summary

Association analysis and QTL analysis based on SNP data identified 21 significant QTL related to carotenoid contents and root color in carrot breeding. Candidate genes related to color evaluation and carotene ratio were suggested, and a DNA marker was developed to distinguish color differences in carrot breeding lines. This study contributes to understanding carotenoid biosynthesis and accumulation in orange carrots.