From QTL to Gene: Building a Genetic Foundation for Maize Biofortification.

For millions of people in developing countries, plant-based foods are the major source of provitamin A carotenoids and vitamin E tocochromanols. More than 125 million preschool-aged children are vitamin A deficient in developing countries, with an estimated 250,000 to 500,000 of them becoming blind every year. Although clinical vitamin E deficiency is rare, suboptimal dietary intake of vitamin E at levels that are associated with an increased risk for cardiovascular disease have been reported in specific population segments of the US and developing countries. Maize is an important staple crop in many of the countries where these nutritional deficiencies are present and has considerable genetic variation for carotenoid and tocochromanol grain levels. However, the varieties of maize grain typically used for human consumption do not provide adequate daily levels of provitamin A and vitamin E. Nearly 17,000 high-pressure liquid chromatography runs were conducted to determine the genetic basis of more than 40 carotenoid and tocochromanol grain traits in the 5,000 member maize nested association mapping panel. Utilizing 28 million single nucleotide polymorphisms (SNPs), our genome-wide association study (GWAS) revealed contrasting genetic architectures between the carotenoid and tocochromanol traits. While a substantial proportion of QTL identified for carotenoids coincided with the genomic position of known carotenoid biosynthetic pathway genes, most of the tocochromanol-related QTL were not associated with known genes from the tocochromanol biosynthetic pathway. Even though all of these biochemical grain traits were highly heritable, a greater number of QTL were identified for tocochromanols relative to carotenoids. Taken together, these results suggest a simpler genetic architecture for carotenoid traits that is possibly due to the recent evolution of this pathway in maize endosperm. Notably, many of the QTL identified for carotenoids were also associated with orange kernel color intensity, implying that visual selection for dark orange kernel color could be enhanced with allele-specific marker-assisted selection for provitamin A carotenoids. Ultimately, our dissection of these two pathways supports future allele mining studies for development of nutrient dense maize.