Setaria-pan-genome

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Setaria-pan-genome

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Here, we de novo assembled 110 representative Setaria accessions from a worldwide collected 1,844 variteies, and performed pan-/graph- genome studies, as well as demographic and genetic studies of Setaria.

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# Setaria-pan-genome

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.

# Content
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
# Citation

# Contacts
Qiang He (qiangh@163.com)

Ornob Alam (oa832@nyu.edu)

Setaria-pan-genome

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