Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet
Jinfeng Chen, Yang Liu, Minxuan Liu, Wenlei Guo, Yongqiang Wang, Qiang He, Weiyao Chen, Yi Liao, Wei Zhang, Yuanzhu Gao, Kongjun Dong, Ruiyu Ren, Tianyu Yang, Liyuan Zhang, Mingyu Qi, Zhiguang Li, Min Zhao, Haigang Wang, Junjie Wang, Zhijun Qiao, Haiquan Li, Yanmiao Jiang, Guoqing Liu, Xiaoqiang Song, Yarui Deng, Hao Li, Feng Yan, Yang Dong, Qingquan Li, Tao Li, Wenyao Yang, Jianghui Cui, Hongru Wang, Yongfeng Zhou, Xiaoming Zhang, Guanqing Jia, Ping Lü, Hui Zhi, Sha Tang, Xianmin Diao
Abstract
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.