# Genotype × environment interactions underlying geographic divergence in carotenoid accumulation and kernel pigmentation of foxtail millet

## TL;DR

This study explores how genetic and environmental factors influence carotenoid levels and kernel color in foxtail millet across different regions.

## Contribution

The study identifies a geographically distinctive carotenoid biomarker and quantifies genotype-by-environment interactions in foxtail millet quality.

## Key findings

- Moderate climate and fertile soils correlate with higher carotenoid content and yellow kernel color.
- Genotype explains 53.39–67.71% of variation in quality traits, with G×E interactions accounting for 16.51–26.40%.
- A unique carotenoid, zeaxanthin-myristate-palmitate, was identified as a regional biomarker in foxtail millet.

## Abstract

Foxtail millet (Setaria italica L.), a drought-resistant cereal crop, is nutritionally valued for its carotenoid-rich kernels that significantly influence both commercial quality and health benefits. While carotenoid content and kernel pigmentation are known to be affected by genotype and environment, the mechanisms governing these relationships remain unclear. This study systematically examined the ecological and genetic determinants of geographical variation in kernel color and carotenoid accumulation patterns across diverse production regions.

The regions with moderate climates (effective accumulated temperature: 1602–1694 °C; precipitation: 373–404 mm) and fertile soils produced higher carotenoid content and more yellow kernel. In contrast, two regions were delineated as thermally constrained zones, exhibiting non-optimal growing conditions with effective accumulated temperatures and diurnal temperature fluctuation. The key environmental drivers of quality variation included effective accumulated temperature, precipitation, soil total phosphorus, and organic matter, though cultivar-specific sensitivity to these factors varied significantly. Variance component analysis demonstrated that genotype was the predominant source of variation, explaining 53.39–67.71% of the total variance, while the G×E interaction accounted for 16.51–26.40%. Furthermore, GGE (Genotype plus Genotype-by-Environment Interaction) biplot analysis revealed distinct genotype-environment interactions: high-performing cultivars in terms of millet quality but less stable with varied locations were optimal for premium regions with relatively higher quality indicators, while environmentally resilient cultivars proved more suitable for marginal regions with relatively lower quality indicators. By Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry method, we detected 39 carotenoid metabolites in foxtail millet kernels, showing significant regional variations, and a geographically distinctive biomarker (zeaxanthin-myristate-palmitate) was identified.

The findings highlight the importance of matching cultivars to regional ecological conditions to optimize foxtail millet quality. These findings provided theoretical foundations for optimizing regional cultivation strategies and improving foxtail millet quality under G×E interactions.

The online version contains supplementary material available at 10.1186/s12870-025-08008-1.