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

Nature Genetics， 2023,  IF 30.80

DOI:10.1038/s41588-023-01423-w

ABSTRACT:

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.