Here, we de novo assembled 110 representative Setaria accessions from a worldwide collection of 1,844 varieties. We establish the importance of pan-genome variation in foxtail millet domestication and improvement for important agronomic traits. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments. Our work identifies key agronomic genes and marker panels for foxtail millet improvement at different geographic sites; these can be used in marker assisted breeding, genomic selection and/or genome editing that can accelerate crop improvement to meet agricultural demands under different climatic conditions.
Pipelines and relevant scripts for:
- Genome assembly
- Genome annotation
- Genomic prediction/selection
- Graph genome construction
- Phylogenetics
- Population genomics and Demographic inference
Data
- 15,758 high confidence TE derived PAVs
Qiang He (qiangh@163.com)
Ornob Alam (oa832@nyu.edu)