The next generation of carotenoid studies in carrot (Daucus carota L.)

Orange carrot (Daucus carota L.) is one of the richest sources of naturally occurring β-carotene while red and yellow carrot varieties contain large quantities of lycopene and lutein. The human body utilizes carotenoids, particularly β-carotene (provitamin A) as a precursor for the production of retinol, which is imperative for normal vision. Further, lycopene has been associated with a lowered risk of prostate cancer in men and a reduction of heart disease, while lutein can cause a significant reduction in the risk for cataract and age-related macular degeneration. Until recently, understanding the regulation and accumulation of carotenoids in carrot was limited by the amount of genomic resources available, with all previous studies focusing on characterized carotenoid biosynthesis genes. Here we demonstrate the utility of Genotyping-by-Sequencing (GBS) to develop genome-wide markers in a carrot mapping population segregating for β-carotene accumulation. Phenotypic data for β-carotene accumulation was acquired using visual assessment and High Performance Liquid Chromatography (HPLC). Employing GBS, in conjunction with the Universal Network Enabled Analysis Kit (UNEAK) TASSEL pipeline, we identified 37,361 novel SNPs. After filtering for missing data, a genetic linkage map was constructed using 569 high-quality SNPs with an average distance of 1.3 cM between markers. β-carotene accumulation was mapped to a 1.1 cM region on the distal end of Chromosome 7 with the closest marker located 0.4 cM away. Increased understanding of the genetic regulation of carotenoids, through the use of next generation technologies, will help plant breeders and researchers improve existing carrot varieties by enhancing their health promoting qualities.