Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

Vitamin A deficiency remains prevalent in parts of Asia, Latin America and sub-Saharan Africa where maize is a food staple. Extensive natural variation exists for carotenoids in maize grain; to understand its genetic basis, we conducted a joint linkage and genome-wide association study in the U.S. maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were expression QTL (eQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six eQTL also had the largest percent phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these eQTL had highly correlated QTL allelic effect estimates across multiple traits, suggesting that pleiotropy within this pathway is largely regulated at the expression level. Significant pairwise epistatic interactions were also detected. These findings provide the most comprehensive genome-level understanding of the genetic and molecular control of carotenoids in any plant system, and a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extensible to other cereals.