Structural variation in the GH1 promoter regulates the hull color of rice

Chengxing Du, Hao Wang, Guangrong Zhong, Xilan Yan, Kehan Di, Longkang Li, Senhai Zhang, Nangu Yang, Yangkai Wang, Weilan Chen, Hua Yuan, Bin Tu, Jiawei Xiong, Zhaohui Zhong, Yuping Wang, Shigui Li, Peng Qin, Bingtian Ma

Molecular Breeding, Volume45, Issue6, 29 May 2025（IF=2.6）

Abstract

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) qHC3.2 on chromosome 3. In this QTL, we identified a 7.3 kb natural structural variation (SV) in the Golden Hull 1 (GH1) promoter region, which suppresses the expression of GH1 and leads to the golden hull phenotype. We have screened seven germplasm resources that contain this natural variation. By introducing GH1™ 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.