文献类型： 外文期刊

作者： He, Qiang ¹ ; Tang, Sha ¹ ; Zhi, Hui ¹ ; Chen, Jinfeng ² ; Zhang, Jun ¹ ; Liang, Hongkai ¹ ; Alam, Ornob ³ ; Li, Hongbo ⁴ ; Zhang, Hui ¹ ; Xing, Lihe ¹ ; Li, Xukai ⁶ ; Zhang, Wei ¹ ; Wang, Hailong ¹ ; Shi, Junpeng ⁷ ; Du, Huilong ⁹ ; Wu, Hongpo ¹ ; Wang, Liwei ¹ ; Yang, Ping ¹ ; Xing, Lu ¹⁰ ; Yan, Hongshan ¹⁰ ; Song, Zhongqiang ¹⁰ ; Liu, Jinrong ¹⁰ ; Wang, Haigang ¹¹ ; Tian, Xiang ¹¹ ; Qiao, Zhijun ¹¹ ; Feng, Guojun ¹ ; Guo, Ruifeng ¹ ; Zhu, Wenjuan ¹ ; Ren, Yuemei ¹ ; Hao, Hongbo ¹ ; Li, Mingzhe ¹ ; Zhang, Aiying ¹ ; Guo, Erhu ¹ ; Yan, Feng ¹ ; Li, Qingquan ¹ ; Liu, Yanli ¹ ; Tian, Bohong ¹ ; Zhao, Xiaoqin ¹ ; Jia, Ruiling ¹ ; Feng, Baili ⁵ ; Zhang, Jiewei ¹ ; Wei, Jianhua ¹ ; Lai, Jinsheng ⁷ ; Jia, Guanqing ¹ ; Purugganan, Michael ³ ; Diao, Xianmin ¹ ;

作者机构： 1.Chinese Acad Agr Sci, Inst Crop Sci, Beijing, Peoples R China

2.Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects &, Beijing, Peoples R China

3.NYU, Ctr Genom & Syst Biol, New York, NY 10012 USA

4.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Genome Anal Lab,M, Shenzhen, Peoples R China

5.Northwest A&F Univ, Coll Agron, Yangling, Peoples R China

6.Shanxi Agr Univ, Coll Life Sci, Taigu, Peoples R China

7.China Agr Univ, State Key Lab Plant Physiol & Biochem, Beijing, Peoples R China

8.China Agr Univ, Natl Maize Improvement Ctr, Dept Plant Genet & Breeding, Beijing, Peoples R China

9.Hebei Univ, Inst Life Sci & Green Dev, Sch Life Sci, Baoding, Peoples R China

10.Anyang Acad Agr Sci, Anyang, Peoples R China

11.Shanxi Agr Univ, Ctr Agr Genet Resources Res, Taiyuan, Peoples R China; Xinjiang Acad Agr Sci, Res Inst Cereal Crops, Urumqi, Peoples R China; Shanxi Agr Univ, Inst High Latitude Crops, Datong, Peoples R China; Hebei Acad Agr & Forestry Sci, Inst Dry Land Farming, Hengshui, Peoples R China; Shanxi Agr Univ, Millet Res Inst, Changzhi, Peoples R China; Qiqihar Sub Acad Heilongjiang Acad Agr Sci, Qiqihar, Peoples R China; Cangzhou Acad Agr & Forestry Sci, Cangzhou, Peoples R China; Dingxi Acad Agr Sci, Dingxi, Peoples R China; Beijing Acad Agr & Forestry Sci, Beijing Key Lab Agr Genet Resources & Biotechnol, Beijing, Peoples R China; New York Univ Abu Dhabi, Ctr Genom & Syst Biol, Abu Dhabi, U Arab Emirates

期刊名称：NATURE GENETICS （ 影响因子：30.8； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2023 年 55 卷 7 期

页码：

收录情况： SCI

摘要： Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions. Setaria pan-genome constructed using genome assemblies of 110 representative accessions and variation analyses provides insights into foxtail millet domestication and the genetic basis for crop improvement.