Nutraceutical foods enriched with phytonutrients such as carotenoids and anthocyanins are highly beneficial for human nutrition and health. To develop foods with improved nutritional quality and health-promoting properties, we have been employing genetic and genomic approaches for novel gene discovery and identifying the factors important for phytonutrient accumulation. By using unique orange and purple cauliflower mutants as models, we have isolated the Orange and Purple gene responsible for the color phenotypes and uncovered novel mechanisms underlying carotenoid and anthocyanin accumulation in food crops. Furthermore, we have demonstrated that these genes can serve as new genetic tools for crop nutritional quality improvement. Introduction of the Orange gene into potato plants not only leads to an enhanced carotenoid level in the tubers, but also continuously stimulates beta-carotene accumulation during long term cold storage. The beta-carotene formed was found to be bioavailable for better human nutrition. Through genome-wide profiling of gene expression by RNA-seq in conjunction with proteomics analysis in a number of carotenoid rich crops, we are in the process to identify the factors that are crucial for high level of phytonutrient accumulation for developing more nutritious and healthy nutraceutical foods.