TheSetaria viridisgenome and diversity panel enables discovery of a novel domestication gene

AbstractDiverse wild and weedy crop relatives hold genetic variants underlying key evolutionary innovations of crops under domestication. Here, we provide genome resources and probe the genetic basis of domestication traits in green millet (Setaria viridis), a close wild relative of foxtail millet (S. italica). Specifically, we develop and exploit a platinum-quality genome assembly andde novoassemblies for 598 wild accessions to identify loci underlying a) response to climate, b) a key ‘loss of shattering’ trait that permits mechanical harvest, and c) leaf angle, a major predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validatedLess Shattering1(SvLES1) as a novel gene for seed shattering, which is rendered non-functional via a retrotransposon insertion inSiLes1, the domesticated loss-of-shattering allele ofS. italica. Together these results and resources projectS. viridisas a key model species for complex trait dissection and biotechnological improvement of panicoid crops.