Carrots (Daucus carota) are a unique model for the accumulation of carotenoids. Beta-carotene accumulates in large amounts in the taproot if the proper alleles of the following three loci are present: OR, Y, and Y2. These three loci are not carotenoid biosynthetic genes but rather post-transcriptional regulation of carotenoid accumulation. The genes underlying the OR and Y loci have been characterized, but the gene underlying the Y2 locus is unknown. Through genomic and transcriptomic analyses, a single candidate that may interact with light signaling was found. To determine the function of this gene, the functional transcript from wild carrot was overexpressed in orange carrots and used in a transient infiltration assay with a GFP fusion tag in tobacco. The orange allele of this gene has a large transposon insertion that theoretically inactivates the gene. However, full length transcript can still be detected in orange carrots. This begs the question of whether the transposon is still active in certain accessions. In this study, the proportion properly assembled Y2 transcript was analyzed via qRT-PCR. A KASP marker was also developed to assist plant breeders in selection for the Y2 locus.
