数字农科院2.0

Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet

文献类型： 外文期刊

作者： Chen, Jinfeng;Liu, Yang;Liu, Minxuan;Guo, Wenlei;Wang, Yongqiang;He, Qiang;Chen, Weiyao;Liao, Yi;Zhang, Wei;Gao, Yuanzhu;Dong, Kongjun;Ren, Ruiyu;Yang, Tianyu;Zhang, Liyuan;Qi, Mingyu;Li, Zhiguang;Zhao, Min;Wang, Haigang;Wang, Junjie;Qiao, Zhijun;Li, Haiquan;Jiang, Yanmiao;Liu, Guoqing;Song, Xiaoqiang;Deng, Yarui;Li, Hai;Yan, Feng;Dong, Yang;Li, Qingquan;Li, Tao;Yang, Wenyao;Cui, Jianghui;Wang, Hongru;Zhou, Yongfeng;Zhang, Xiaoming;Jia, Guanqing;Lu, Ping;Zhi, Hui;Tang, Sha;Diao, Xianmin

作者机构：

期刊名称： NATURE GENETICS

ISSN： 1061-4036

年卷期： 2023 年

页码：

收录情况： SCIE（2023版）

摘要： Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet. Population analysis of 516 wild and domesticated broomcorn millet genomes and a graph-based pangenome based on de novo assemblies of 32 representative accessions identify genomic variations associated with domestication traits.

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