The Origin of Orange Pigment in Carrot

A better understanding of plant domestication provides insight into the historical interaction between plants and people. Additionally, understanding the location and timing of domestication events can guide genetic diversity preservation, identify regions of the genome under selection and ultimately improve crops. A recent study, along with the support of historical documentation, identified Central Asia as the likely region of carrot (Daucus carota L.) domestication. However, several questions remain including: 1) what is the extent of linkage disequilibrium in carrot, 2) what regions of the genome were impacted during domestication and 3) where did the secondary domestication, which lead to the accumulation of alpha- and beta-carotene, of carrot occur? We have utilized Genotyping-by-Sequencing, in conjugation with the newly sequenced carrot genome, on a diversity panel consisting of 332 wild and domesticated samples and have generated over 34,000 genome-wide SNPs. Here we present preliminary phylogeny, population structure, linkage disequilibrium, nucleotide diversity and F_ST results. Furthermore, we explore haplotype diversity in regions associated with carotenoid accumulation and begin to elucidate the geographic origin(s) of orange pigmentation in carrot.