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

文献类型： 外文期刊

第一作者： He, Qiang

作者： He, Qiang;Tang, Sha;Zhi, Hui;Zhang, Jun;Liang, Hongkai;Zhang, Hui;Xing, Lihe;Zhang, Wei;Wang, Hailong;Wu, Hongpo;Wang, Liwei;Yang, Ping;Jia, Guanqing;Diao, Xianmin;Chen, Jinfeng;Alam, Ornob;Purugganan, Michael;Li, Hongbo;Zhang, Hui;Feng, Baili;Li, Xukai;Shi, Junpeng;Lai, Jinsheng;Shi, Junpeng;Lai, Jinsheng;Du, Huilong;Xing, Lu;Yan, Hongshan;Song, Zhongqiang;Liu, Jinrong;Wang, Haigang;Tian, Xiang;Qiao, Zhijun

作者机构：

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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