Genomic investigation of 18,421 lines reveals the genetic architecture of rice

• 成果类型: Article
• 署名作者: Wei, Xin; Chen, Mengjiao; Zhang, Qi; Gong, Junyi; Liu, Jie; Yong, Kaicheng; Wang, Qin; Fan, Jiongjiong; Chen, Suhui; Hua, Hua; Luo, Zhaowei; Zhao, Xiaoyan; Wang, Xuan; Li, Wei; Cong, Jia; Yu, Xiting; Wang, Zhihan; Huang, Ruipeng; Chen, Jiaxin; Zhou, Xiaoyi; Qiu, Jie; Xu, Ping; Murray, Jeremy; Wang, Hai; Xu, Yang; Xu, Chenwu; Xu, Gen; Yang, Jinliang; Han, Bin; Huang, Xuehui
• 署名单位: Shanghai Normal University; Chinese Academy of Agricultural Sciences; China National Rice Research Institute, CAAS; Chinese Academy of Sciences; Center for Excellence in Molecular Plant Sciences, CAS; China Agricultural University; Yangzhou University; University of Nebraska System; University of Nebraska Lincoln
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-12855
• DOI: 10.1126/science.adm8762
• 发表日期: 2024-07-05
• 关键词: wide association; agronomic traits; heritability; phenotypes; epistasis; annotation; SYSTEM

摘要

Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.