AbstractThe bran is a nutritive fraction of the maize (Zea maysL.) kernel containing micronutrients, quality protein, and antioxidants beneficial for human health. Bran consists of two major components: aleurone and pericarp. Increasing this nutritive fraction would therefore have implications on biofortification of maize. Since quantification of these two layers is difficult, the goals of this study were to develop efficient techniques for analyzing these layers and to develop molecular markers for pericarp and aleurone yield. Two populations with various characteristics were genotyped using genotyping-by-sequencing. The first was a yellow corn population with contrasting pericarp thicknesses. The second was a blue corn population segregating forIntensifier1alleles. Both populations segregated for the multiple aleurone layer (MAL) trait that is known to increase aleurone yield. In this study, it was found that MALs are mostly determined by a locus on chromosome 8, but several minor loci are also involved. The inheritance of MALs was complex and seemingly more additive than dominant. In the blue corn population, anthocyanin content increased 20 to 30% with the addition of MALs demonstrating its effectiveness at increasing aleurone yield. Elemental analysis was performed on MAL lines and indicated a role of MALs in increasing iron content in the grain. Iron content was increased 17.5% in the MAL lines over the single aleurone layer lines and 35.5% over the recurrent parent, Mo17. Zinc content was increased 15.5% in the MAL lines compared to the recurrent parent. QTL analyses are presented in this study on many pericarp, aleurone, and grain quality traits. Molecular markers were also tested for the MAL locus on chromosome 8, and candidate genes are discussed. Results of this study may assist plant breeders enhancing anthocyanin content and other beneficial phytonutrients in maize.