Uncovering Genetic Architecture and Genomic Prediction of Vitamin E Content in Tropical Maize

Vitamin E (tocochromanols), a vital lipid-soluble antioxidant, is often deficient in maize-based diets. Our objective was to identify potential genomic regions associated with tocochromanols variation and evaluate the potential of genomic predictions for its improvement. We assessed 1044 tropical maize inbreds from three panels across multiple environments, and genotyped them with high-density single-nucleotide polymorphisms. Across panels, we identified 50 causal loci, including 15 in a combined panel associated with three grain tocochromanol components. Associated loci showed strong positive allelic effects (1.12- to 2.72-fold increment due to favourable allele) for improving tocochromanol content. Notably, four loci were associated with α-tocotrienol, and three loci with α-tocopherol were found to be stable, and one pleiotropic locus influenced both. Underlying candidate genes are enriched in cellular, catalytic, biosynthetic and metabolic processes, with 14 involved in the tocochromanol biosynthesis pathway. Favourable haplotypes on chromosomes 5 and 7, notably increased α-tocopherol (6.12-16.19 µg/g) and γ-tocopherol (32.12-102.31 µg/g) levels, respectively. Genomic prediction models proved useful in predicting tocochromanols with moderate-to-high prediction accuracies (0.43-0.52), demonstrating their potential to develop elite, high-tocochromanol lines. Our results provided valuable insights into the genetic architecture of tocochromanols and support accelerating biofortification through genome-wide selection to improve vitamin E levels in tropical maize.