Introduction:

Setaria italica (foxtail millet) is an ideal model for C4 photosynthetic crop plants. Despite its favorable traits, genomic diversity and potential for genetic enhancement remain relatively understudied. Through high throughput sequencing, 110 core-set reference-level genomes were assembled, facilitating the establishment of a complete pan-genome and the construction of a graph-based genome for Setaria. Large-scale genetic studies across 68 traits in 13 environments identified potential genes for millet improvement in diverse geographic locations. These findings can inform marker-assisted breeding, genomic selection, and genome editing to expedite crop improvement under various climatic conditions.