# Genetic Dissection of Carotenoid Variation by Integrating Quantitative Trait Loci Mapping and Candidate Region Association Study in Sweet Corn

## TL;DR

This study identifies genetic factors influencing carotenoid levels in sweet corn, offering tools to improve its nutritional value.

## Contribution

Integration of QTL mapping and association study reveals key genes and SNPs linked to carotenoid content in sweet corn.

## Key findings

- Fifteen QTLs across chromosomes 5-9 explain 3.83–17.25% of carotenoid variation.
- A major-effect QTL cluster on chromosome 6 regulates multiple carotenoids.
- Zm00001d036238, a GDSL esterase/lipase gene, is strongly associated with β-cryptoxanthin accumulation.

## 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.