Structural variation in the promoter regulates the hull color of rice.

Unlabelled: Rice hull color (HC) is crucial for improving the mechanization efficiency of hybrid rice seed production. However, the genetic resources for hull color currently available for practical production are limited, highlighting an urgent need to explore natural variations that can be utilized in breeding. In this study, we conducted a genome-wide association study (GWAS) on the hull color of 301 rice germplasm resources and identified a significant quantitative trait locus (QTL) on chromosome 3. In this QTL, we identified a 7.3 kb natural structural variation (SV) in the  ( promoter region, which suppresses the expression of and leads to the golden hull phenotype. We have screened seven germplasm resources that contain this natural variation. By introducing ™ into U1S, the hull color of U1S™ remains stable and is unaffected by drying time, demonstrating its potential value for breeding applications. Our study provides valuable natural variations and germplasm resources for the mechanized production of hybrid rice.

Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-025-01569-x.