Elemental Accumulation in Kernels of the Maize Nested Association Mapping Panel Reveals Signals of Gene by Environment Interactions

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.