A graph-based genome and pan-genome variation of the model plant Setaria

• Published in: Nature genetics Vol. 55; no. 7; pp. 1232 - 1242
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: United States Nature Publishing Group 01.07.2023; Nature Publishing Group US
• Subjects: Breeding; Cereal crops; Climatic conditions; Crop improvement; Crops; Domestication; Gene expression; Gene families; Genes; Genetic diversity; Genome editing; Genomes; Genomics; Millet; Photosynthesis; Phylogenetics; Setaria; Setaria italica
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/s41588-023-01423-w

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.