qiangh06/setaria-pan-genome

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.

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 ([email protected])

Ornob Alam ([email protected])