The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene

We present a platinum-quality genome assembly for the model grass Setaria viridis, and high quality genomic sequences of 600+ wild accessions (average 42.6x coverage). Presence-absence variation (PAV) and single-nucleotide polymorphisms (SNPs) identify several subpopulations in North America. Using genome-wide association mapping plus CRISPR-Cas9 technology, we identified and validated Less Shattering1 (SvLES1), a gene for seed shattering with a retrotransposon insertion in the domesticated S. italica (foxtail millet) allele. We also identified a candidate gene for erect leaves, orthologous to the maize gene liguleless2. These results demonstrate the utility of the model plant S. viridis for complex trait dissection in panicoid crops.