Elemental accumulation in seeds is the product of a combination of environment and a wide variety of genetically controlled physiological processes. We measured the kernel elemental composition of the Nested Association Mapping (NAM) of maize ( Zea mays L.) grown in 4 different environments. Analysis of variance revealed strong effects of genotype, environment and genotype by environment interactions. Using Joint-linkage mapping on a set of 7000 markers we identified 354 quantitative trait loci (QTL) across 20 elements, four environments and a combination of the environments. Leveraging 20 M SNPs derived from genome resequencing on the parents of the population, genome-wide association mapping studies (GWAS) detected 8573 loci. While most of the GWAS SNPs were located near genes not previously implicated in elemental regulation, several SNPs were located next to orthologs of well-characterized elemental regulation genes.

Rapid development and adoption of biofortified, provitamin A-dense orange maize (Zea maysL.) varieties could be facilitated by a greater understanding of the natural variation underlying kernel color, including as relates to carotenoid biosynthesis and retention in maize grain. Greater abundance of carotenoids in maize kernels is generally accompanied by deeper orange color, useful for distinguishing provitamin A-dense varieties to consumers. While kernel color can be scored and selected with high-throughput, low-cost phenotypic methods within breeding selection programs, it remains to be well established as to what would be the logical genetic loci to target for selection for kernel color. We conducted a genome-wide association study of maize kernel color, as determined by colorimetry, in 1,651 yellow and orange inbreds from the Ames maize inbred panel. Associations were found withy1, encoding the first committed step in carotenoid biosynthesis, and withdxs2, which encodes the enzyme responsible for the first committed step in the biosynthesis of the isoprenoid precursors of carotenoids. These genes logically could contribute to overall carotenoid abundance and thus kernel color. ThelcyEandzep1genes, which can affect carotenoid composition, were also found to be associated with colorimeter values. A pathway-level analysis, focused on genes witha priorievidence of involvement in carotenoid biosynthesis and retention, revealed associations fordxs3anddmes1, involved in isoprenoid biosynthesis;ps1andvp5, within the core carotenoid pathway; andvp14, involved in cleavage of carotenoids. Collectively, these identified genes appear relevant to the accumulation of kernel color.