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.
分类号:
- 相关文献
作者其他论文 更多>>
-
Study of the flavor dissipation mechanism of soy-sauce-marinated beef using flavor matrices
作者:Wang, Jingfan;Yang, Ping;Liu, Junmei;Qiang, Yu;Han, Dong;Zhang, Chunhui;Wang, Jingfan;Liu, Junmei;Purcaro, Giorgia;Fauconnier, Marie-Laure;Yang, Weifang;Jia, Wei
关键词:Soy sauce-based marinated beef; Cooling processing; Sensory-directed flavor analysis; Odor activity value; Aroma-active compound
-
Ammonia-oxidizing archaea bacteria (AOB) and comammox drive the nitrification in alkaline soil under long-term biochar and N fertilizer applications
作者:Sun, Jiali;Sun, Jiali;Li, Hongbo;Zhang, Aiping;Rengel, Zed;Rengel, Zed;Zhou, Yizhen
关键词:Long -term biochar application; Ammonia-oxidizing archaea and bacteria; Complete ammonia oxidizers; Soil nitrification rate
-
Heat-induced aggregation behavior of wheat gluten after adding citrus pectin with different esterification degree
作者:Shi, Wanlu;Chen, Jinfeng;Cui, Yanli;Zhang, Shenggui;Ma, Yunxiang;Chen, Jinfeng;Zhang, Shenggui;Liu, Jia;Chen, Jinfeng;Zhang, Shenggui
关键词:Wheat gluten; Heat-induced; Aggregation behavior; Pectin; Degree of esterification
-
Methylglyoxal scavenging capacity of fiber-bound polyphenols from highland barley during colonic fermentation and its modulation on methylglyoxal-interfered gut microbiota
作者:Li, Jinxin;Zhu, Ling;Wu, Gangcheng;Zhang, Hui;Zhang, Hao;Liu, Wei;Yang, Xijuan;Zhang, Hui
关键词:Bound phenolic compounds; Methylglyoxal; Gut microbiota; Colonic fermentation; Scavenging capacity
-
Yield loss of inferior crop species and its physiological mechanism in a semiarid cereal-legume intercropping system
作者:Wang, Wei;Li, Meng-Ying;Zhang, Wei;Rehman, Muhammad Maqsood Ur;Wang, Bao-Zhong;Ullah, Fazal;Cheng, Zheng-Guo;Zhu, Li;Tao, Hong-Yan;Xiong, You-Cai;Zhao, Jian-Hua;Zhang, Jin-Lin;Wang, Wen-Ying;Xiong, You-Cai
关键词:Water competition; Intercropping; Rainfed agroecosystem; Yield formation; Remobilization
-
Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data
作者:Zhang, Wei;Liu, Linqing;Zhou, Mei;Su, Shiguang;Dong, Lin;Meng, Xinxin;Li, Xueting;Wang, Chonglong;Zhang, Wei;Liu, Linqing;Zhou, Mei;Su, Shiguang;Wang, Chonglong;Zhang, Wei;Liu, Linqing;Zhou, Mei;Su, Shiguang;Dong, Lin;Meng, Xinxin;Li, Xueting;Wang, Chonglong
关键词:Wanbei pig; Asian wild boar; selection signatures; fixation index (FST); polymorphism levels (theta pi); whole genome resequencing
-
Overexpression of lncRNA77580 Regulates Drought and Salinity Stress Responses in Soybean
作者:Chen, Xiangqian;Jiang, Xuemin;Niu, Fengjuan;Sun, Xianjun;Hu, Zheng;Zhang, Hui;Jiang, Qiyan;Gao, Fei
关键词:soybean; drought stress; salt stress; long non-coding RNA