Natural Variation of PH8 Allele Improves Architecture and Cold Tolerance in Rice
2025
Cheng Chen | Xia Zhang | Jialin Chen | Mingjia Xu | Weiying Zhao | Yangkai Wang | Zhuo Chen | Jiawei Xiong | Hua Yuan | Weilan Chen | Bin Tu | Ting Li | Liangzhu Kang | Shiwen Tang | Yuping Wang | Bingtian Ma | Shigui Li | Peng Qin
Abstract Empirical breeding efforts targeting cold tolerance and ideal plant architecture have significantly improved yield and facilitated the geographic expansion of japonica rice cultivation. However, the genetic drivers and underlying molecular mechanisms of these traits remain insufficiently understood. Here, we identify Plant Height 8 (PH8) as a key gene regulating both plant stature and cold stress response in rice. Genome wide association analysis (GWAS), supported by functional validation, shows that loss of PH8 reduces plant height without affecting other agronomic traits. Notably, we found that PH8 also negatively regulates cold tolerance. A prevalent haplotype, PH8 Hap.0 , exhibits reduced PH8 expression due to natural variation in its promoter region, resulting in shorter plants and enhanced cold tolerance. Selective sweep and geographic distribution analyses indicate that PH8 Hap.0 originated in high-latitude regions and underwent strong directional selection during modern japonica improvement. Functional assays demonstrate that PH8 enhances cold tolerance via improved reactive oxygen species (ROS) scavenging by repressing APX2, an antioxidant gene involved in ROS detoxification. Our findings reveal PH8 as a dual regulator of plant architecture and cold stress adaptation, and highlight PH8 Hap.0 as a historically selected allele that contributed to the climatic adaptation and geographical expansion of japonica rice.
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