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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
This version of the manuscript includes a revised introduction, additional assays for shattering, and substantial expansion of the population genetics section; major changes to the latter include assessment of presence/absence variation and tests for selection. The author list has been slightly modified. Figures 1-4 have been replaced and additional supplemental figures and tables have been provided.