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

Abstract

Diverse 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 and de novo assemblies 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 validated Less Shattering1 (SvLES1) as a novel gene for seed shattering, which is rendered non-functional via a retrotransposon insertion in SiLes1, the domesticated loss-of-shattering allele of S. italica. Together these results and resources project S. viridis as a key model species for complex trait dissection and biotechnological improvement of panicoid crops.