Epistatic interactions underlying orange pigmentation in carrot (Daucus carota L.)

Orange carrots (Daucus carota ssp. sativus) are an important source of provitamin A carotenoids, unlike their wild progenitor D. carota ssp. carota. Until recently the basis of orange pigmentation was thought to be controlled primarily by two genes, Y and Y-2, however, the use of an association panel with high density SNP markers led to the discovery of an additional candidate carotenoid presence gene, Or. In other plants, Or homologs function to differentiate protoplastids into chromoplasts, which provide a sink for carotenoids. Additionally, Or post-transcriptionally regulates Phytoene Synthase (PSY), the most important regulatory enzyme in the carotenoid pathway. We genotyped a diverse collection of modern and historic domesticated cultivars and wild carrot accessions to explore the epistatic interactions between Or, Y, and Y-2 to better understand how these genes contribute to the presence of orange pigmentation. We find that orange pigmentation is best predicted when the genotypes of Or and Y-2 are known and that Y is less predictive. Furthermore, carotenoid presence is maximized when Or is homozygous dominant and Y-2 is homozygous recessive. Our results pave the way for creating a robust marker-assisted selection strategy for orange pigmentation in carrot breeding programs.