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.
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