Abstract
Sweet corn is widely cultivated and valued for its palatability and nutritional quality, with kernels accumulating substantial carotenoids, which serve as essential antioxidants and vitamin A precursors. This study elucidated the genetic basis of carotenoid variation in sweet corn kernels by integrating quantitative trait loci (QTL) mapping with a candidate region association study. Seven carotenoid-related traits were quantified in a recombinant inbred line (RIL) population and its parental lines. QTL mapping based on a high-density genotyping-by-target sequencing (GBTS) map and BLUE values across two environments identified 15 loci on chromosomes 5, 6, 7, 8, and 9, explaining 3.83-17.25% of the phenotypic variance. Notably, chromosome 6 harbored a cluster of major-effect QTLs regulating β-cryptoxanthin, zeaxanthin, lutein, total carotenoids, and provitamin A contents. A regional association study within these linkage-defined intervals detected 71 significant SNPs (Bonferroni p < 1/n) and identified Zm00001d036238, encoding a GDSL esterase/lipase, as a strong candidate gene associated with β-cryptoxanthin accumulation. This gene exhibited kernel-specific expression in the endosperm and harbored a downstream cis-variant (Chr6: 78,466,427) correlated with increased carotenoid content. Allelic effect analysis indicated that the A/A genotype conferred markedly higher β-cryptoxanthin levels than other genotypes. Collectively, these findings provide valuable genetic resources for marker-assisted selection and biofortification breeding to enhance the nutritional quality of sweet corn.