A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants

文献类型： 外文期刊

第一作者： Wang, Tianyi

作者： Wang, Tianyi;He, Wenchuang;Li, Xiaoxia;Zhang, Chao;He, Huiying;Yuan, Qiaoling;Zhang, Bin;Zhang, Hong;Leng, Yue;Wei, Hua;Xu, Qiang;Shi, Chuanlin;Liu, Xiangpei;Guo, Mingliang;Wang, Xianmeng;Chen, Wu;Zhang, Zhipeng;Yang, Longbo;Lv, Yang;Qian, Hongge;Zhang, Bintao;Yu, Xiaoman;Liu, Congcong;Cao, Xinglan;Cui, Yan;Zhang, Qianqian;Dai, Xiaofan;Zhou, Yongfeng;Ruan, Jue;Qian, Qian;Shang, Lianguang;Wang, Tianyi;Wang, Tianyi;Guo, Longbiao;Wang, Yuexing;Qian, Qian;Qian, Qian;Shang, Lianguang

作者机构：

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：14.9； 五年影响因子：16.4 ）

ISSN： 0305-1048

年卷期： 2023 年

页码：

收录情况： SCI

摘要： Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a large rice population with a total of 10 548 accessions to construct a rice super-population variation map (RSPVM), consisting of 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations and 184 736 presence/absence variations . Assessment of variation detection efficiency for different population sizes revealed a sharp increase of all types of variation as the population size increased and a gradual saturation of that after the population size reached 10 000. Variant frequency analysis indicated that similar to 90% of the obtained variants were rare, and would therefore likely be difficult to detect in a relatively small population. Among the rare variants, only 2.7% were predicted to be deleterious. Population structure, genetic diversity and gene functional polymorphism of this large population were evaluated based on different subsets of RSPVM, demonstrating the great potential of RSPVM for use in downstream applications. Our study provides both a rich genetic basis for understanding natural rice variations and a powerful tool for exploiting great potential of rare variants in future rice research, including population genetics and functional genomics. [GRAPHICS]

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